Starting phenix.real_space_refine on Tue Apr 29 18:10:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n78_24223/04_2025/7n78_24223_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n78_24223/04_2025/7n78_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_24223/04_2025/7n78_24223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n78_24223/04_2025/7n78_24223.map" model { file = "/net/cci-nas-00/data/ceres_data/7n78_24223/04_2025/7n78_24223_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n78_24223/04_2025/7n78_24223_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 9, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 6, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 18} 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: 5.62, per 1000 atoms: 0.73 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: 2.52 Conformation dependent library (CDL) restraints added in 898.6 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: 1.00 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: 3.22 Time building geometry restraints manager: 2.60 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.080 Find NCS groups from input model: 0.080 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:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (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 TRP 0.010 0.002 TRP A 100 HIS 0.009 0.001 HIS A 385 PHE 0.015 0.002 PHE A1154 TYR 0.015 0.002 TYR A 235 ARG 0.039 0.002 ARG A 720 Details of bonding type rmsd hydrogen bonds : bond 0.16580 ( 443) hydrogen bonds : angle 6.66547 ( 1266) covalent geometry : bond 0.01005 ( 7813) covalent geometry : angle 0.95950 (10658) 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 : 0.856 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.0944 time to fit residues: 60.3461 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 : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 30.0000 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 40.0000 chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.100373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069410 restraints weight = 16839.928| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.21 r_work: 0.2900 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1229 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= 0.139 Angle : 0.535 6.298 10658 Z= 0.269 Chirality : 0.041 0.149 1300 Planarity : 0.005 0.059 1330 Dihedral : 9.161 76.221 1415 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.09 % Allowed : 8.46 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1016 helix: 1.08 (0.23), residues: 490 sheet: -0.14 (0.41), residues: 163 loop : -0.36 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 253 HIS 0.005 0.001 HIS A 817 PHE 0.011 0.001 PHE A1051 TYR 0.017 0.001 TYR A 931 ARG 0.007 0.000 ARG A1159 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 443) hydrogen bonds : angle 4.76833 ( 1266) covalent geometry : bond 0.00312 ( 7813) covalent geometry : angle 0.53464 (10658) Misc. bond : bond 0.00273 ( 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 45 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.877 Fit side-chains REVERT: A 102 LEU cc_start: 0.9374 (mm) cc_final: 0.9047 (tp) REVERT: A 905 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7647 (pmm) outliers start: 8 outliers final: 3 residues processed: 41 average time/residue: 1.1145 time to fit residues: 49.9579 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 : 0.860 ------------------------------------------------------------------------------- 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 51 optimal weight: 50.0000 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 30.0000 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.100066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069206 restraints weight = 16950.799| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.25 r_work: 0.2891 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1605 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 : 0.503 7.123 10658 Z= 0.250 Chirality : 0.040 0.138 1300 Planarity : 0.004 0.062 1330 Dihedral : 8.685 71.168 1415 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.36 % Allowed : 9.82 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1016 helix: 1.74 (0.24), residues: 491 sheet: 0.02 (0.41), residues: 163 loop : 0.03 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 253 HIS 0.002 0.000 HIS A 817 PHE 0.012 0.001 PHE A1051 TYR 0.015 0.001 TYR A 235 ARG 0.004 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 443) hydrogen bonds : angle 4.38473 ( 1266) covalent geometry : bond 0.00290 ( 7813) covalent geometry : angle 0.50314 (10658) Misc. bond : bond 0.00171 ( 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 50 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.886 Fit side-chains REVERT: A 102 LEU cc_start: 0.9340 (mm) cc_final: 0.9004 (tp) REVERT: A 205 MET cc_start: 0.8847 (mtm) cc_final: 0.8568 (mtm) REVERT: A 232 LEU cc_start: 0.8739 (mp) cc_final: 0.8510 (tt) REVERT: A 521 MET cc_start: 0.7414 (mmt) cc_final: 0.7084 (mmt) REVERT: A 905 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7767 (pmm) outliers start: 10 outliers final: 1 residues processed: 47 average time/residue: 0.9504 time to fit residues: 49.1901 Evaluate side-chains 36 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR 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 18 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 92 optimal weight: 0.0570 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.100764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.070096 restraints weight = 16957.819| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.25 r_work: 0.2915 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7814 Z= 0.099 Angle : 0.477 6.917 10658 Z= 0.236 Chirality : 0.039 0.131 1300 Planarity : 0.004 0.064 1330 Dihedral : 8.237 69.521 1415 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.77 % Allowed : 10.64 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.27), residues: 1016 helix: 2.14 (0.24), residues: 492 sheet: 0.28 (0.40), residues: 163 loop : 0.18 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.002 0.000 HIS A 408 PHE 0.011 0.001 PHE A1051 TYR 0.013 0.001 TYR A 931 ARG 0.003 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 443) hydrogen bonds : angle 4.15625 ( 1266) covalent geometry : bond 0.00221 ( 7813) covalent geometry : angle 0.47747 (10658) Misc. bond : bond 0.00170 ( 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: 13 poor density : 37 time to evaluate : 0.904 Fit side-chains REVERT: A 102 LEU cc_start: 0.9319 (mm) cc_final: 0.8997 (tp) REVERT: A 201 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8326 (tm) REVERT: A 205 MET cc_start: 0.8846 (mtm) cc_final: 0.8489 (mtm) REVERT: A 232 LEU cc_start: 0.8715 (mp) cc_final: 0.8502 (tt) REVERT: A 521 MET cc_start: 0.7253 (mmt) cc_final: 0.7014 (mmt) REVERT: A 905 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7631 (pmm) outliers start: 13 outliers final: 4 residues processed: 45 average time/residue: 0.8577 time to fit residues: 42.6420 Evaluate side-chains 40 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 449 LEU Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 997 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 74 optimal weight: 0.0070 chunk 92 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.100783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.069982 restraints weight = 16762.662| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.24 r_work: 0.2926 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 7814 Z= 0.100 Angle : 0.467 7.262 10658 Z= 0.230 Chirality : 0.039 0.135 1300 Planarity : 0.004 0.064 1330 Dihedral : 7.990 69.253 1415 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.77 % Allowed : 11.60 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.27), residues: 1016 helix: 2.29 (0.24), residues: 492 sheet: 0.44 (0.41), residues: 163 loop : 0.26 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 170 HIS 0.002 0.000 HIS A 408 PHE 0.009 0.001 PHE A1123 TYR 0.012 0.001 TYR A 931 ARG 0.003 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 443) hydrogen bonds : angle 4.07357 ( 1266) covalent geometry : bond 0.00229 ( 7813) covalent geometry : angle 0.46683 (10658) Misc. bond : bond 0.00168 ( 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 50 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.786 Fit side-chains REVERT: A 102 LEU cc_start: 0.9288 (mm) cc_final: 0.8972 (tp) REVERT: A 201 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8362 (tm) REVERT: A 205 MET cc_start: 0.8832 (mtm) cc_final: 0.8467 (mtm) REVERT: A 232 LEU cc_start: 0.8646 (mp) cc_final: 0.8437 (tt) REVERT: A 521 MET cc_start: 0.7436 (mmt) cc_final: 0.7183 (mmt) REVERT: A 905 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7585 (pmm) outliers start: 13 outliers final: 5 residues processed: 48 average time/residue: 0.8366 time to fit residues: 44.4692 Evaluate side-chains 43 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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 997 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 66 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 69 optimal weight: 0.0970 chunk 48 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.100437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.069687 restraints weight = 16682.401| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.22 r_work: 0.2909 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 : 0.002 0.046 7814 Z= 0.108 Angle : 0.485 9.533 10658 Z= 0.234 Chirality : 0.040 0.137 1300 Planarity : 0.004 0.063 1330 Dihedral : 7.759 68.292 1415 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.77 % Allowed : 12.41 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.27), residues: 1016 helix: 2.40 (0.23), residues: 493 sheet: 0.66 (0.41), residues: 157 loop : 0.34 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 170 HIS 0.001 0.000 HIS A 817 PHE 0.009 0.001 PHE A 940 TYR 0.012 0.001 TYR A 931 ARG 0.003 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 443) hydrogen bonds : angle 4.01428 ( 1266) covalent geometry : bond 0.00250 ( 7813) covalent geometry : angle 0.48476 (10658) Misc. bond : bond 0.00165 ( 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 50 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.841 Fit side-chains REVERT: A 102 LEU cc_start: 0.9280 (mm) cc_final: 0.8943 (tp) REVERT: A 201 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8433 (tm) REVERT: A 205 MET cc_start: 0.8799 (mtm) cc_final: 0.8442 (mtm) REVERT: A 232 LEU cc_start: 0.8710 (mp) cc_final: 0.8500 (tt) REVERT: A 345 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8899 (pt) REVERT: A 521 MET cc_start: 0.7517 (mmt) cc_final: 0.7309 (mmt) REVERT: A 714 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8042 (mt) REVERT: A 905 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7706 (pmm) outliers start: 13 outliers final: 5 residues processed: 47 average time/residue: 0.8167 time to fit residues: 42.6477 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 : 0.838 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 30.0000 chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 40 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.098936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068232 restraints weight = 16830.523| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.22 r_work: 0.2878 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7814 Z= 0.153 Angle : 0.504 8.295 10658 Z= 0.245 Chirality : 0.040 0.136 1300 Planarity : 0.004 0.063 1330 Dihedral : 7.735 65.727 1415 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.77 % Allowed : 12.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.27), residues: 1016 helix: 2.35 (0.23), residues: 493 sheet: 0.69 (0.42), residues: 155 loop : 0.31 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 253 HIS 0.001 0.000 HIS A 817 PHE 0.012 0.001 PHE A 531 TYR 0.011 0.001 TYR A 931 ARG 0.004 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 443) hydrogen bonds : angle 4.08098 ( 1266) covalent geometry : bond 0.00360 ( 7813) covalent geometry : angle 0.50436 (10658) Misc. bond : bond 0.00154 ( 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 47 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.858 Fit side-chains REVERT: A 201 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8460 (tm) REVERT: A 205 MET cc_start: 0.8846 (mtm) cc_final: 0.8476 (mtm) REVERT: A 232 LEU cc_start: 0.8734 (mp) cc_final: 0.8531 (tt) REVERT: A 449 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7153 (tm) REVERT: A 521 MET cc_start: 0.7573 (mmt) cc_final: 0.7347 (mmt) REVERT: A 714 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8068 (mt) REVERT: A 905 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7785 (pmm) outliers start: 13 outliers final: 4 residues processed: 45 average time/residue: 0.8490 time to fit residues: 42.3158 Evaluate side-chains 41 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.099862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.069031 restraints weight = 16915.069| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.25 r_work: 0.2901 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7814 Z= 0.110 Angle : 0.488 8.985 10658 Z= 0.235 Chirality : 0.040 0.136 1300 Planarity : 0.004 0.063 1330 Dihedral : 7.519 63.994 1415 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.36 % Allowed : 13.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.27), residues: 1016 helix: 2.46 (0.23), residues: 492 sheet: 0.80 (0.42), residues: 155 loop : 0.35 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.001 0.000 HIS A 817 PHE 0.009 0.001 PHE A 940 TYR 0.011 0.001 TYR A 931 ARG 0.003 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 443) hydrogen bonds : angle 4.02226 ( 1266) covalent geometry : bond 0.00254 ( 7813) covalent geometry : angle 0.48789 (10658) Misc. bond : bond 0.00157 ( 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 44 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.913 Fit side-chains REVERT: A 449 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7144 (tm) REVERT: A 521 MET cc_start: 0.7558 (mmt) cc_final: 0.7342 (mmt) REVERT: A 714 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8090 (mt) REVERT: A 894 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7721 (mm-30) REVERT: A 905 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7675 (pmm) outliers start: 10 outliers final: 4 residues processed: 43 average time/residue: 1.0107 time to fit residues: 47.6864 Evaluate side-chains 40 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR 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 87 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 92 optimal weight: 0.0470 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.099063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.068165 restraints weight = 17068.293| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.25 r_work: 0.2881 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7814 Z= 0.143 Angle : 0.535 11.195 10658 Z= 0.251 Chirality : 0.040 0.138 1300 Planarity : 0.004 0.063 1330 Dihedral : 7.455 63.040 1415 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.77 % Allowed : 12.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.27), residues: 1016 helix: 2.37 (0.23), residues: 498 sheet: 0.79 (0.43), residues: 155 loop : 0.42 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 253 HIS 0.001 0.000 HIS A 817 PHE 0.009 0.001 PHE A 940 TYR 0.011 0.001 TYR A 235 ARG 0.004 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 443) hydrogen bonds : angle 4.05852 ( 1266) covalent geometry : bond 0.00335 ( 7813) covalent geometry : angle 0.53527 (10658) Misc. bond : bond 0.00149 ( 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 47 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.772 Fit side-chains REVERT: A 345 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8912 (pt) REVERT: A 449 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7158 (tm) REVERT: A 521 MET cc_start: 0.7667 (mmt) cc_final: 0.7430 (mmt) REVERT: A 714 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8108 (mt) REVERT: A 894 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 905 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7759 (pmm) REVERT: A 997 LEU cc_start: 0.8132 (mm) cc_final: 0.7910 (mm) outliers start: 13 outliers final: 5 residues processed: 45 average time/residue: 0.9332 time to fit residues: 46.0434 Evaluate side-chains 43 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 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 79 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 0.0870 chunk 94 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 1 optimal weight: 20.0000 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.100240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069616 restraints weight = 16828.839| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.24 r_work: 0.2910 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7814 Z= 0.098 Angle : 0.512 12.499 10658 Z= 0.241 Chirality : 0.040 0.148 1300 Planarity : 0.004 0.062 1330 Dihedral : 7.297 64.642 1415 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.36 % Allowed : 12.96 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.27), residues: 1016 helix: 2.48 (0.23), residues: 492 sheet: 0.85 (0.43), residues: 150 loop : 0.45 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.002 0.000 HIS A 817 PHE 0.008 0.001 PHE A 940 TYR 0.012 0.001 TYR A 931 ARG 0.003 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03008 ( 443) hydrogen bonds : angle 4.00771 ( 1266) covalent geometry : bond 0.00222 ( 7813) covalent geometry : angle 0.51161 (10658) Misc. bond : bond 0.00160 ( 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: 10 poor density : 36 time to evaluate : 0.762 Fit side-chains REVERT: A 205 MET cc_start: 0.8797 (mtm) cc_final: 0.8526 (mtm) REVERT: A 345 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8918 (pt) REVERT: A 449 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7157 (tm) REVERT: A 521 MET cc_start: 0.7641 (mmt) cc_final: 0.7411 (mmt) REVERT: A 714 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8081 (mt) REVERT: A 894 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7373 (mm-30) REVERT: A 905 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7725 (pmm) outliers start: 10 outliers final: 5 residues processed: 44 average time/residue: 0.8889 time to fit residues: 42.9343 Evaluate side-chains 45 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 95 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 0.0970 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 0.0570 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.100611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069934 restraints weight = 16809.970| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.25 r_work: 0.2924 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7814 Z= 0.097 Angle : 0.516 13.134 10658 Z= 0.242 Chirality : 0.040 0.172 1300 Planarity : 0.004 0.063 1330 Dihedral : 7.081 66.001 1415 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.23 % Allowed : 13.10 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.27), residues: 1016 helix: 2.43 (0.23), residues: 499 sheet: 0.88 (0.43), residues: 150 loop : 0.50 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.001 0.000 HIS A 408 PHE 0.009 0.001 PHE A 940 TYR 0.012 0.001 TYR A 931 ARG 0.003 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 443) hydrogen bonds : angle 3.96861 ( 1266) covalent geometry : bond 0.00222 ( 7813) covalent geometry : angle 0.51565 (10658) Misc. bond : bond 0.00157 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4832.48 seconds wall clock time: 83 minutes 46.50 seconds (5026.50 seconds total)