Starting phenix.real_space_refine on Tue Mar 3 21:35:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n78_24223/03_2026/7n78_24223_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n78_24223/03_2026/7n78_24223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n78_24223/03_2026/7n78_24223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n78_24223/03_2026/7n78_24223.map" model { file = "/net/cci-nas-00/data/ceres_data/7n78_24223/03_2026/7n78_24223_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n78_24223/03_2026/7n78_24223_trim.cif" } resolution = 3.0 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= 0.014 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 4971 2.51 5 N 1283 2.21 5 O 1366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7669 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7441 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PCIS': 3, 'PTRANS': 68, 'TRANS': 958} Chain breaks: 6 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 543 Unresolved non-hydrogen angles: 701 Unresolved non-hydrogen dihedrals: 458 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'ARG:plan': 18, 'TRP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 9, 'GLU:plan': 10, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 295 Chain: "A" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 228 Unusual residues: {' MG': 1, 'LMT': 3, 'PC1': 2, 'PO4': 1, 'SPM': 1, 'Y01': 3} Classifications: {'undetermined': 11, 'water': 3} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.03, per 1000 atoms: 0.26 Number of scatterers: 7669 At special positions: 0 Unit cell: (81.079, 104.765, 133.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 2 15.00 Mg 1 11.99 O 1366 8.00 N 1283 7.00 C 4971 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 324.3 milliseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 8 sheets defined 51.3% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 77 removed outlier: 4.050A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.717A pdb=" N ASP A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 251 through 284 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 397 through 408 Processing helix chain 'A' and resid 417 through 445 Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.937A pdb=" N VAL A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 removed outlier: 4.458A pdb=" N CYS A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR A 476 " --> pdb=" O MET A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.801A pdb=" N ASN A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.540A pdb=" N ARG A 540 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 651 through 657 removed outlier: 3.888A pdb=" N VAL A 655 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 695 through 700 removed outlier: 3.648A pdb=" N GLN A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.876A pdb=" N VAL A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.896A pdb=" N VAL A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 821 through 832 Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 850 through 863 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 877 through 884 Processing helix chain 'A' and resid 909 through 948 removed outlier: 3.683A pdb=" N MET A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 963 Processing helix chain 'A' and resid 963 through 974 removed outlier: 3.756A pdb=" N THR A 968 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1020 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.838A pdb=" N PHE A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A1061 " --> pdb=" O ALA A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1073 through 1092 Processing helix chain 'A' and resid 1108 through 1145 removed outlier: 3.644A pdb=" N PHE A1127 " --> pdb=" O PHE A1123 " (cutoff:3.500A) Proline residue: A1138 - end of helix Processing helix chain 'A' and resid 1152 through 1164 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.111A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 176 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 303 removed outlier: 4.354A pdb=" N CYS A 291 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS A 312 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 387 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.491A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.576A pdb=" N GLY A 887 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N SER A 903 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER A 889 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 868 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE A 888 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N MET A 870 " --> pdb=" O ILE A 888 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA A 741 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N PHE A 846 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N MET A 743 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS A 767 " --> pdb=" O HIS A 817 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ALA A 819 " --> pdb=" O HIS A 767 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 769 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU A 768 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 530 through 531 removed outlier: 3.974A pdb=" N ALA A 530 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 527 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL A 520 " --> pdb=" O ARG A 720 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG A 720 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 714 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA A 637 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL A 619 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 559 443 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1596 1.33 - 1.45: 1554 1.45 - 1.57: 4583 1.57 - 1.69: 12 1.69 - 1.81: 68 Bond restraints: 7813 Sorted by residual: bond pdb=" C31 PC1 A1206 " pdb=" O31 PC1 A1206 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C21 PC1 A1206 " pdb=" O21 PC1 A1206 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C21 PC1 A1210 " pdb=" O21 PC1 A1210 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" O1 PO4 A1201 " pdb=" P PO4 A1201 " ideal model delta sigma weight residual 1.565 1.471 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" O3 PO4 A1201 " pdb=" P PO4 A1201 " ideal model delta sigma weight residual 1.569 1.478 0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 7808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 10453 2.95 - 5.89: 163 5.89 - 8.84: 29 8.84 - 11.79: 9 11.79 - 14.73: 4 Bond angle restraints: 10658 Sorted by residual: angle pdb=" CAM Y01 A1205 " pdb=" CAY Y01 A1205 " pdb=" OAW Y01 A1205 " ideal model delta sigma weight residual 111.19 125.92 -14.73 3.00e+00 1.11e-01 2.41e+01 angle pdb=" CAM Y01 A1211 " pdb=" CAY Y01 A1211 " pdb=" OAW Y01 A1211 " ideal model delta sigma weight residual 111.19 125.83 -14.64 3.00e+00 1.11e-01 2.38e+01 angle pdb=" CAM Y01 A1204 " pdb=" CAY Y01 A1204 " pdb=" OAW Y01 A1204 " ideal model delta sigma weight residual 111.19 125.69 -14.50 3.00e+00 1.11e-01 2.34e+01 angle pdb=" N THR A 341 " pdb=" CA THR A 341 " pdb=" C THR A 341 " ideal model delta sigma weight residual 113.28 118.72 -5.44 1.22e+00 6.72e-01 1.99e+01 angle pdb=" N SER A 339 " pdb=" CA SER A 339 " pdb=" C SER A 339 " ideal model delta sigma weight residual 111.40 106.30 5.10 1.22e+00 6.72e-01 1.75e+01 ... (remaining 10653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4427 16.07 - 32.13: 335 32.13 - 48.20: 82 48.20 - 64.26: 21 64.26 - 80.33: 5 Dihedral angle restraints: 4870 sinusoidal: 1896 harmonic: 2974 Sorted by residual: dihedral pdb=" CA PRO A1026 " pdb=" C PRO A1026 " pdb=" N LEU A1027 " pdb=" CA LEU A1027 " ideal model delta harmonic sigma weight residual -180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR A 866 " pdb=" C TYR A 866 " pdb=" N CYS A 867 " pdb=" CA CYS A 867 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ASN A1042 " pdb=" CB ASN A1042 " pdb=" CG ASN A1042 " pdb=" OD1 ASN A1042 " ideal model delta sinusoidal sigma weight residual 120.00 -165.51 -74.49 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 4867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1053 0.075 - 0.151: 223 0.151 - 0.226: 14 0.226 - 0.301: 4 0.301 - 0.377: 6 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CBG Y01 A1211 " pdb=" CAQ Y01 A1211 " pdb=" CBD Y01 A1211 " pdb=" CBI Y01 A1211 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CBG Y01 A1204 " pdb=" CAQ Y01 A1204 " pdb=" CBD Y01 A1204 " pdb=" CBI Y01 A1204 " both_signs ideal model delta sigma weight residual False -2.33 -2.69 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CBG Y01 A1205 " pdb=" CAQ Y01 A1205 " pdb=" CBD Y01 A1205 " pdb=" CBI Y01 A1205 " both_signs ideal model delta sigma weight residual False -2.33 -2.69 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1297 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 750 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" CD GLN A 750 " 0.056 2.00e-02 2.50e+03 pdb=" OE1 GLN A 750 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN A 750 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 720 " -0.098 9.50e-02 1.11e+02 4.82e-02 6.20e+00 pdb=" NE ARG A 720 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 720 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG A 720 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 720 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 202 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" CD GLN A 202 " 0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN A 202 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN A 202 " -0.013 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 42 2.52 - 3.12: 5657 3.12 - 3.71: 11696 3.71 - 4.31: 16556 4.31 - 4.90: 28750 Nonbonded interactions: 62701 Sorted by model distance: nonbonded pdb=" OD2 ASP A 508 " pdb="MG MG A1202 " model vdw 1.930 2.170 nonbonded pdb=" O2 PO4 A1201 " pdb="MG MG A1202 " model vdw 1.950 2.170 nonbonded pdb=" OH TYR A 235 " pdb=" O PRO A 465 " model vdw 2.134 3.040 nonbonded pdb=" OE1 GLU A 766 " pdb=" NE2 HIS A 817 " model vdw 2.154 3.120 nonbonded pdb=" O THR A 510 " pdb="MG MG A1202 " model vdw 2.245 2.170 ... (remaining 62696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.410 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.013 0.775 7814 Z= 0.995 Angle : 0.960 14.735 10658 Z= 0.445 Chirality : 0.064 0.377 1300 Planarity : 0.005 0.053 1330 Dihedral : 13.024 80.326 2948 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -1.34 (0.24), residues: 1016 helix: -0.59 (0.21), residues: 481 sheet: -0.38 (0.41), residues: 157 loop : -1.31 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.002 ARG A 720 TYR 0.015 0.002 TYR A 235 PHE 0.015 0.002 PHE A1154 TRP 0.010 0.002 TRP A 100 HIS 0.009 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.01005 ( 7813) covalent geometry : angle 0.95950 (10658) hydrogen bonds : bond 0.16580 ( 443) hydrogen bonds : angle 6.66547 ( 1266) Misc. bond : bond 0.77502 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.311 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.5621 time to fit residues: 30.6638 Evaluate side-chains 31 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 40.0000 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.100504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.069558 restraints weight = 16923.786| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.23 r_work: 0.2903 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7814 Z= 0.134 Angle : 0.534 6.583 10658 Z= 0.268 Chirality : 0.041 0.148 1300 Planarity : 0.005 0.059 1330 Dihedral : 9.169 76.259 1415 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.23 % Allowed : 8.19 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.54 (0.26), residues: 1016 helix: 1.13 (0.23), residues: 490 sheet: -0.14 (0.41), residues: 163 loop : -0.32 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1159 TYR 0.017 0.001 TYR A 931 PHE 0.011 0.001 PHE A1051 TRP 0.007 0.001 TRP A 253 HIS 0.005 0.001 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7813) covalent geometry : angle 0.53375 (10658) hydrogen bonds : bond 0.03782 ( 443) hydrogen bonds : angle 4.71222 ( 1266) Misc. bond : bond 0.00101 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.266 Fit side-chains REVERT: A 102 LEU cc_start: 0.9372 (mm) cc_final: 0.9053 (tp) REVERT: A 521 MET cc_start: 0.7006 (mmt) cc_final: 0.6801 (mmt) REVERT: A 905 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7651 (pmm) outliers start: 9 outliers final: 3 residues processed: 42 average time/residue: 0.4742 time to fit residues: 21.6507 Evaluate side-chains 38 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 905 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 100 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A1042 ASN A1122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.067266 restraints weight = 16901.737| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.22 r_work: 0.2850 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7814 Z= 0.198 Angle : 0.548 6.899 10658 Z= 0.271 Chirality : 0.042 0.138 1300 Planarity : 0.004 0.063 1330 Dihedral : 8.759 67.531 1415 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.36 % Allowed : 10.37 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.11 (0.27), residues: 1016 helix: 1.65 (0.23), residues: 490 sheet: -0.03 (0.41), residues: 163 loop : -0.03 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 740 TYR 0.017 0.001 TYR A 235 PHE 0.011 0.001 PHE A 832 TRP 0.007 0.001 TRP A 253 HIS 0.002 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 7813) covalent geometry : angle 0.54790 (10658) hydrogen bonds : bond 0.03827 ( 443) hydrogen bonds : angle 4.47236 ( 1266) Misc. bond : bond 0.00194 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.300 Fit side-chains REVERT: A 102 LEU cc_start: 0.9330 (mm) cc_final: 0.8983 (tp) REVERT: A 205 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8491 (mtm) REVERT: A 232 LEU cc_start: 0.8796 (mp) cc_final: 0.8539 (tt) REVERT: A 521 MET cc_start: 0.7158 (mmt) cc_final: 0.6860 (mmt) REVERT: A 905 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7764 (pmm) outliers start: 10 outliers final: 2 residues processed: 43 average time/residue: 0.4252 time to fit residues: 19.9520 Evaluate side-chains 40 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 905 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 3 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 30.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1042 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.099283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068435 restraints weight = 17117.877| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.24 r_work: 0.2878 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7814 Z= 0.126 Angle : 0.494 6.658 10658 Z= 0.244 Chirality : 0.040 0.134 1300 Planarity : 0.004 0.065 1330 Dihedral : 8.365 64.230 1415 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.36 % Allowed : 11.73 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.53 (0.27), residues: 1016 helix: 2.00 (0.23), residues: 492 sheet: 0.22 (0.41), residues: 163 loop : 0.13 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 740 TYR 0.014 0.001 TYR A 931 PHE 0.011 0.001 PHE A1051 TRP 0.006 0.001 TRP A 253 HIS 0.002 0.000 HIS A 817 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7813) covalent geometry : angle 0.49390 (10658) hydrogen bonds : bond 0.03339 ( 443) hydrogen bonds : angle 4.25202 ( 1266) Misc. bond : bond 0.00156 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.275 Fit side-chains REVERT: A 102 LEU cc_start: 0.9322 (mm) cc_final: 0.9006 (tp) REVERT: A 201 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8399 (tm) REVERT: A 205 MET cc_start: 0.8824 (mtm) cc_final: 0.8490 (mtm) REVERT: A 232 LEU cc_start: 0.8824 (mp) cc_final: 0.8572 (tt) REVERT: A 521 MET cc_start: 0.7315 (mmt) cc_final: 0.7072 (mmt) REVERT: A 905 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7751 (pmm) outliers start: 10 outliers final: 2 residues processed: 47 average time/residue: 0.3896 time to fit residues: 20.0782 Evaluate side-chains 40 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 935 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.0570 chunk 94 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.099857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.069085 restraints weight = 16821.322| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.23 r_work: 0.2898 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7814 Z= 0.109 Angle : 0.475 7.659 10658 Z= 0.234 Chirality : 0.040 0.142 1300 Planarity : 0.004 0.064 1330 Dihedral : 7.925 63.438 1415 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.32 % Allowed : 11.46 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.86 (0.27), residues: 1016 helix: 2.27 (0.24), residues: 492 sheet: 0.38 (0.40), residues: 168 loop : 0.28 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 740 TYR 0.013 0.001 TYR A 931 PHE 0.010 0.001 PHE A1051 TRP 0.006 0.001 TRP A 170 HIS 0.002 0.000 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7813) covalent geometry : angle 0.47521 (10658) hydrogen bonds : bond 0.03113 ( 443) hydrogen bonds : angle 4.09575 ( 1266) Misc. bond : bond 0.00157 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.298 Fit side-chains REVERT: A 102 LEU cc_start: 0.9291 (mm) cc_final: 0.8979 (tp) REVERT: A 201 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8385 (tm) REVERT: A 205 MET cc_start: 0.8832 (mtm) cc_final: 0.8473 (mtm) REVERT: A 232 LEU cc_start: 0.8744 (mp) cc_final: 0.8527 (tt) REVERT: A 345 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8896 (pt) REVERT: A 449 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7231 (tm) REVERT: A 521 MET cc_start: 0.7413 (mmt) cc_final: 0.7126 (mmt) REVERT: A 905 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7672 (pmm) outliers start: 17 outliers final: 4 residues processed: 50 average time/residue: 0.3523 time to fit residues: 19.4945 Evaluate side-chains 42 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 89 optimal weight: 0.0170 chunk 93 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.099845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.069093 restraints weight = 16910.498| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.25 r_work: 0.2899 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7814 Z= 0.110 Angle : 0.477 7.784 10658 Z= 0.234 Chirality : 0.040 0.136 1300 Planarity : 0.004 0.064 1330 Dihedral : 7.731 62.726 1415 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.18 % Allowed : 12.55 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.03 (0.27), residues: 1016 helix: 2.36 (0.23), residues: 492 sheet: 0.67 (0.43), residues: 155 loop : 0.33 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 740 TYR 0.012 0.001 TYR A 931 PHE 0.009 0.001 PHE A 940 TRP 0.005 0.001 TRP A 170 HIS 0.002 0.000 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7813) covalent geometry : angle 0.47739 (10658) hydrogen bonds : bond 0.03066 ( 443) hydrogen bonds : angle 4.06413 ( 1266) Misc. bond : bond 0.00158 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 0.296 Fit side-chains REVERT: A 102 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8934 (tp) REVERT: A 201 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8488 (tm) REVERT: A 205 MET cc_start: 0.8832 (mtm) cc_final: 0.8497 (mtm) REVERT: A 232 LEU cc_start: 0.8706 (mp) cc_final: 0.8485 (tt) REVERT: A 345 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8906 (pt) REVERT: A 449 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7172 (tm) REVERT: A 521 MET cc_start: 0.7449 (mmt) cc_final: 0.7144 (mmt) REVERT: A 714 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8048 (mt) REVERT: A 905 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7670 (pmm) outliers start: 16 outliers final: 4 residues processed: 47 average time/residue: 0.3703 time to fit residues: 19.2037 Evaluate side-chains 44 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 59 optimal weight: 20.0000 chunk 49 optimal weight: 50.0000 chunk 89 optimal weight: 0.0060 chunk 44 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.100321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.069676 restraints weight = 16962.340| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.26 r_work: 0.2914 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7814 Z= 0.096 Angle : 0.477 8.134 10658 Z= 0.230 Chirality : 0.039 0.140 1300 Planarity : 0.004 0.064 1330 Dihedral : 7.549 62.995 1415 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.18 % Allowed : 12.28 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.15 (0.27), residues: 1016 helix: 2.46 (0.23), residues: 492 sheet: 0.75 (0.42), residues: 155 loop : 0.38 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 740 TYR 0.013 0.001 TYR A 931 PHE 0.008 0.001 PHE A1051 TRP 0.006 0.001 TRP A 170 HIS 0.002 0.000 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 7813) covalent geometry : angle 0.47736 (10658) hydrogen bonds : bond 0.02954 ( 443) hydrogen bonds : angle 4.00901 ( 1266) Misc. bond : bond 0.00160 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 102 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8909 (tp) REVERT: A 201 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8514 (tm) REVERT: A 205 MET cc_start: 0.8827 (mtm) cc_final: 0.8482 (mtm) REVERT: A 232 LEU cc_start: 0.8733 (mp) cc_final: 0.8519 (tt) REVERT: A 345 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8915 (pt) REVERT: A 449 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7140 (tm) REVERT: A 521 MET cc_start: 0.7451 (mmt) cc_final: 0.7122 (mmt) REVERT: A 714 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8058 (mt) REVERT: A 905 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7685 (pmm) outliers start: 16 outliers final: 4 residues processed: 50 average time/residue: 0.4289 time to fit residues: 23.3347 Evaluate side-chains 46 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.0470 chunk 87 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.100655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.069933 restraints weight = 16984.783| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.28 r_work: 0.2914 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7814 Z= 0.098 Angle : 0.492 9.390 10658 Z= 0.236 Chirality : 0.039 0.136 1300 Planarity : 0.004 0.063 1330 Dihedral : 7.413 63.085 1415 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.77 % Allowed : 13.10 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.22 (0.27), residues: 1016 helix: 2.51 (0.23), residues: 493 sheet: 0.80 (0.43), residues: 150 loop : 0.43 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 740 TYR 0.012 0.001 TYR A 931 PHE 0.008 0.001 PHE A 940 TRP 0.006 0.001 TRP A 170 HIS 0.002 0.000 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 7813) covalent geometry : angle 0.49152 (10658) hydrogen bonds : bond 0.02921 ( 443) hydrogen bonds : angle 3.97789 ( 1266) Misc. bond : bond 0.00160 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 102 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8909 (tp) REVERT: A 201 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8539 (tm) REVERT: A 205 MET cc_start: 0.8813 (mtm) cc_final: 0.8463 (mtm) REVERT: A 345 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8919 (pt) REVERT: A 449 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7135 (tm) REVERT: A 521 MET cc_start: 0.7450 (mmt) cc_final: 0.7108 (mmt) REVERT: A 714 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8089 (mt) REVERT: A 894 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7714 (mm-30) REVERT: A 905 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7679 (pmm) outliers start: 13 outliers final: 4 residues processed: 48 average time/residue: 0.4387 time to fit residues: 22.9576 Evaluate side-chains 46 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.099979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.069425 restraints weight = 16788.975| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.23 r_work: 0.2906 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7814 Z= 0.110 Angle : 0.509 12.102 10658 Z= 0.239 Chirality : 0.040 0.138 1300 Planarity : 0.004 0.065 1330 Dihedral : 7.263 62.782 1415 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.64 % Allowed : 12.96 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.24 (0.27), residues: 1016 helix: 2.51 (0.23), residues: 494 sheet: 0.83 (0.43), residues: 150 loop : 0.43 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 740 TYR 0.011 0.001 TYR A 931 PHE 0.008 0.001 PHE A 940 TRP 0.005 0.001 TRP A 170 HIS 0.001 0.000 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7813) covalent geometry : angle 0.50906 (10658) hydrogen bonds : bond 0.02976 ( 443) hydrogen bonds : angle 3.98555 ( 1266) Misc. bond : bond 0.00153 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.315 Fit side-chains REVERT: A 102 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8881 (tp) REVERT: A 201 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8508 (tm) REVERT: A 205 MET cc_start: 0.8818 (mtm) cc_final: 0.8448 (mtm) REVERT: A 449 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7149 (tm) REVERT: A 521 MET cc_start: 0.7467 (mmt) cc_final: 0.7118 (mmt) REVERT: A 714 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8090 (mt) REVERT: A 894 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7705 (mm-30) REVERT: A 905 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7695 (pmm) outliers start: 12 outliers final: 4 residues processed: 46 average time/residue: 0.4214 time to fit residues: 21.1645 Evaluate side-chains 44 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 12 optimal weight: 0.0070 chunk 5 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 83 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070334 restraints weight = 16722.146| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.26 r_work: 0.2931 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7814 Z= 0.090 Angle : 0.506 12.399 10658 Z= 0.238 Chirality : 0.039 0.144 1300 Planarity : 0.004 0.063 1330 Dihedral : 7.051 64.004 1415 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.09 % Allowed : 13.51 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.30 (0.27), residues: 1016 helix: 2.56 (0.23), residues: 494 sheet: 0.88 (0.43), residues: 150 loop : 0.46 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 740 TYR 0.012 0.001 TYR A 931 PHE 0.008 0.001 PHE A 940 TRP 0.007 0.000 TRP A 170 HIS 0.002 0.000 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 7813) covalent geometry : angle 0.50588 (10658) hydrogen bonds : bond 0.02875 ( 443) hydrogen bonds : angle 3.93765 ( 1266) Misc. bond : bond 0.00158 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.278 Fit side-chains REVERT: A 102 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8878 (tp) REVERT: A 201 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8485 (tm) REVERT: A 205 MET cc_start: 0.8810 (mtm) cc_final: 0.8429 (mtm) REVERT: A 521 MET cc_start: 0.7497 (mmt) cc_final: 0.7157 (mmt) REVERT: A 714 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8095 (mt) REVERT: A 894 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 905 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7673 (pmm) outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 0.4322 time to fit residues: 21.2035 Evaluate side-chains 43 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 985 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 40.0000 chunk 47 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1042 ASN A1122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.097251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.066394 restraints weight = 17131.660| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.24 r_work: 0.2837 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7814 Z= 0.226 Angle : 0.600 14.949 10658 Z= 0.285 Chirality : 0.043 0.187 1300 Planarity : 0.004 0.063 1330 Dihedral : 7.361 59.031 1415 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.50 % Allowed : 13.78 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 2.00 (0.27), residues: 1016 helix: 2.21 (0.23), residues: 501 sheet: 0.63 (0.42), residues: 156 loop : 0.48 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 740 TYR 0.013 0.001 TYR A 235 PHE 0.013 0.002 PHE A 832 TRP 0.006 0.001 TRP A 253 HIS 0.003 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 7813) covalent geometry : angle 0.59995 (10658) hydrogen bonds : bond 0.03597 ( 443) hydrogen bonds : angle 4.22265 ( 1266) Misc. bond : bond 0.00134 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.55 seconds wall clock time: 39 minutes 32.20 seconds (2372.20 seconds total)