Starting phenix.real_space_refine on Tue Mar 3 21:47:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n72_24217/03_2026/7n72_24217_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n72_24217/03_2026/7n72_24217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n72_24217/03_2026/7n72_24217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n72_24217/03_2026/7n72_24217.map" model { file = "/net/cci-nas-00/data/ceres_data/7n72_24217/03_2026/7n72_24217_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n72_24217/03_2026/7n72_24217_trim.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 1 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 5001 2.51 5 N 1287 2.21 5 O 1364 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7705 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7475 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PCIS': 3, 'PTRANS': 68, 'TRANS': 958} Chain breaks: 6 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 652 Unresolved non-hydrogen dihedrals: 427 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ARG:plan': 17, '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: 290 Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 230 Unusual residues: {' MG': 1, 'ALF': 1, 'LMT': 3, 'PC1': 2, 'SPM': 1, 'Y01': 3} Classifications: {'undetermined': 11, 'water': 5} Link IDs: {None: 15} 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: 1.91, per 1000 atoms: 0.25 Number of scatterers: 7705 At special positions: 0 Unit cell: (80.773, 104.9, 135.321, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 46 16.00 P 1 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1364 8.00 N 1287 7.00 C 5001 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: 0.67 Conformation dependent library (CDL) restraints added in 305.5 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: 42 helices and 8 sheets defined 52.8% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 59 through 68 removed outlier: 3.799A pdb=" N LEU A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 4.026A 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 removed outlier: 3.640A pdb=" N SER A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 222 through 231 removed outlier: 4.068A pdb=" N ASP A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 285 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 337 through 342 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' 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: 3.728A pdb=" N VAL A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 removed outlier: 4.322A pdb=" N CYS A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR A 476 " --> pdb=" O MET A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.567A pdb=" N GLY A 577 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 695 through 700 removed outlier: 3.577A pdb=" N GLN A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 709 removed outlier: 3.702A pdb=" N VAL A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.519A 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 822 through 832 Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 850 through 864 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 949 removed outlier: 3.576A pdb=" N MET A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 963 Processing helix chain 'A' and resid 963 through 974 Processing helix chain 'A' and resid 993 through 1020 removed outlier: 3.506A pdb=" N ALA A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.787A pdb=" N PHE A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.631A 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 1093 Processing helix chain 'A' and resid 1108 through 1145 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 78 through 79 removed outlier: 3.655A pdb=" N GLU A 91 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.164A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 303 removed outlier: 4.539A pdb=" N CYS A 291 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N CYS A 312 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 387 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.701A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.871A pdb=" N VAL A 868 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE A 888 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N MET A 870 " --> pdb=" O ILE A 888 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA A 741 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N PHE A 846 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET A 743 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER A 821 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ALA A 773 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU A 768 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 519 through 524 removed outlier: 6.838A pdb=" N VAL A 718 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 523 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 716 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER A 633 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG A 622 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 635 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 588 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.768A pdb=" N ALA A 530 " --> pdb=" O LYS A 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 559 467 hydrogen bonds defined for protein. 1317 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: 1.42 Time building geometry restraints manager: 0.89 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: 1975 1.33 - 1.45: 1232 1.45 - 1.57: 4560 1.57 - 1.69: 12 1.69 - 1.81: 72 Bond restraints: 7851 Sorted by residual: bond pdb=" C31 PC1 A1206 " pdb=" O31 PC1 A1206 " ideal model delta sigma weight residual 1.330 1.456 -0.126 2.00e-02 2.50e+03 4.00e+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 3.80e+01 bond pdb=" C21 PC1 A1206 " pdb=" O21 PC1 A1206 " ideal model delta sigma weight residual 1.331 1.452 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.685 1.791 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" CAY Y01 A1211 " pdb=" OAW Y01 A1211 " ideal model delta sigma weight residual 1.332 1.412 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 7846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.66: 10702 13.66 - 27.33: 7 27.33 - 40.99: 0 40.99 - 54.66: 0 54.66 - 68.32: 2 Bond angle restraints: 10711 Sorted by residual: angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F2 ALF A1201 " ideal model delta sigma weight residual 108.68 177.00 -68.32 3.00e+00 1.11e-01 5.19e+02 angle pdb=" F3 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 109.63 173.73 -64.10 3.00e+00 1.11e-01 4.57e+02 angle pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " pdb=" F3 ALF A1201 " ideal model delta sigma weight residual 109.59 87.56 22.03 3.00e+00 1.11e-01 5.39e+01 angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 109.02 87.16 21.86 3.00e+00 1.11e-01 5.31e+01 angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F3 ALF A1201 " ideal model delta sigma weight residual 109.69 89.85 19.84 3.00e+00 1.11e-01 4.37e+01 ... (remaining 10706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4512 17.81 - 35.62: 314 35.62 - 53.43: 55 53.43 - 71.24: 13 71.24 - 89.05: 7 Dihedral angle restraints: 4901 sinusoidal: 1927 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 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PHE A 507 " pdb=" C PHE A 507 " pdb=" N ASP A 508 " pdb=" CA ASP A 508 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA TYR A 251 " pdb=" C TYR A 251 " pdb=" N TYR A 252 " pdb=" CA TYR A 252 " ideal model delta harmonic sigma weight residual -180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1129 0.076 - 0.151: 155 0.151 - 0.227: 13 0.227 - 0.302: 2 0.302 - 0.378: 7 Chirality restraints: 1306 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 3.57e+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 -2.71 0.37 2.00e-01 2.50e+01 3.50e+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 -2.70 0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 1303 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 202 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" CD GLN A 202 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN A 202 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN A 202 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 164 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" CD GLN A 164 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLN A 164 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN A 164 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A1135 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" CD GLN A1135 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLN A1135 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN A1135 " 0.011 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 45 2.56 - 3.14: 5922 3.14 - 3.73: 12096 3.73 - 4.31: 17269 4.31 - 4.90: 28956 Nonbonded interactions: 64288 Sorted by model distance: nonbonded pdb=" F2 ALF A1201 " pdb="MG MG A1202 " model vdw 1.971 2.120 nonbonded pdb=" OD2 ASP A 458 " pdb=" O HOH A1301 " model vdw 2.023 3.040 nonbonded pdb=" OD2 ASP A 508 " pdb="MG MG A1202 " model vdw 2.105 2.170 nonbonded pdb=" O THR A 510 " pdb="MG MG A1202 " model vdw 2.211 2.170 nonbonded pdb=" N1 SPM A1203 " pdb=" O HOH A1302 " model vdw 2.234 3.120 ... (remaining 64283 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.860 Find NCS groups from input model: 0.150 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:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.010 0.661 7852 Z= 0.826 Angle : 1.345 68.320 10711 Z= 0.523 Chirality : 0.059 0.378 1306 Planarity : 0.006 0.043 1335 Dihedral : 13.129 89.046 2979 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: -0.87 (0.24), residues: 1016 helix: -0.20 (0.21), residues: 484 sheet: -0.59 (0.38), residues: 163 loop : -0.87 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.002 ARG A 444 TYR 0.016 0.002 TYR A 931 PHE 0.011 0.002 PHE A1154 TRP 0.010 0.002 TRP A1166 HIS 0.014 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00714 ( 7851) covalent geometry : angle 1.34534 (10711) hydrogen bonds : bond 0.14681 ( 467) hydrogen bonds : angle 6.32723 ( 1317) Misc. bond : bond 0.66122 ( 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 79 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 421 MET cc_start: 0.6989 (mtt) cc_final: 0.5785 (tpt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.5951 time to fit residues: 49.6018 Evaluate side-chains 49 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 0.0370 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074976 restraints weight = 12743.470| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.13 r_work: 0.2871 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7852 Z= 0.134 Angle : 0.847 30.855 10711 Z= 0.346 Chirality : 0.041 0.135 1306 Planarity : 0.005 0.053 1335 Dihedral : 8.714 81.034 1416 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.94 % Allowed : 7.51 % Favored : 91.55 % 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: 0.77 (0.26), residues: 1016 helix: 1.26 (0.23), residues: 486 sheet: -0.23 (0.38), residues: 169 loop : 0.02 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 366 TYR 0.017 0.001 TYR A 931 PHE 0.012 0.001 PHE A1154 TRP 0.011 0.001 TRP A 253 HIS 0.004 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7851) covalent geometry : angle 0.84669 (10711) hydrogen bonds : bond 0.03936 ( 467) hydrogen bonds : angle 4.80723 ( 1317) Misc. bond : bond 0.00084 ( 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 59 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7930 (m-80) cc_final: 0.7315 (m-80) REVERT: A 421 MET cc_start: 0.6992 (mtt) cc_final: 0.5758 (tpt) REVERT: A 521 MET cc_start: 0.8125 (mmm) cc_final: 0.7730 (mmm) REVERT: A 955 ASP cc_start: 0.8967 (m-30) cc_final: 0.8640 (m-30) outliers start: 7 outliers final: 1 residues processed: 57 average time/residue: 0.4100 time to fit residues: 25.4144 Evaluate side-chains 51 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 58 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.072849 restraints weight = 12646.019| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.14 r_work: 0.2834 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7852 Z= 0.190 Angle : 0.857 31.336 10711 Z= 0.350 Chirality : 0.042 0.138 1306 Planarity : 0.005 0.044 1335 Dihedral : 8.221 75.169 1416 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.47 % Allowed : 7.64 % Favored : 90.88 % 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: 1.27 (0.27), residues: 1016 helix: 1.71 (0.23), residues: 485 sheet: 0.08 (0.38), residues: 165 loop : 0.16 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 366 TYR 0.017 0.002 TYR A 931 PHE 0.012 0.002 PHE A1154 TRP 0.010 0.001 TRP A 253 HIS 0.004 0.001 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 7851) covalent geometry : angle 0.85747 (10711) hydrogen bonds : bond 0.04202 ( 467) hydrogen bonds : angle 4.69677 ( 1317) Misc. bond : bond 0.00028 ( 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 63 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.250 Fit side-chains REVERT: A 84 HIS cc_start: 0.7926 (m90) cc_final: 0.7539 (m90) REVERT: A 379 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7908 (mmp-170) REVERT: A 421 MET cc_start: 0.7097 (mtt) cc_final: 0.5821 (tpt) REVERT: A 521 MET cc_start: 0.8138 (mmm) cc_final: 0.7761 (mmm) outliers start: 11 outliers final: 3 residues processed: 57 average time/residue: 0.3820 time to fit residues: 23.7557 Evaluate side-chains 50 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 55 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.074086 restraints weight = 12874.791| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.16 r_work: 0.2888 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7852 Z= 0.135 Angle : 0.820 30.615 10711 Z= 0.330 Chirality : 0.041 0.136 1306 Planarity : 0.004 0.046 1335 Dihedral : 7.820 78.426 1416 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.61 % Allowed : 9.25 % Favored : 89.14 % 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: 485 sheet: -0.05 (0.37), residues: 175 loop : 0.32 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 366 TYR 0.016 0.001 TYR A 931 PHE 0.012 0.001 PHE A1154 TRP 0.009 0.001 TRP A 253 HIS 0.003 0.001 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7851) covalent geometry : angle 0.81972 (10711) hydrogen bonds : bond 0.03667 ( 467) hydrogen bonds : angle 4.53340 ( 1317) Misc. bond : bond 0.00018 ( 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 66 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 84 HIS cc_start: 0.7959 (m90) cc_final: 0.7581 (m90) REVERT: A 178 TYR cc_start: 0.7813 (m-80) cc_final: 0.7199 (m-80) REVERT: A 379 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7804 (mmp-170) REVERT: A 385 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.7360 (p90) REVERT: A 421 MET cc_start: 0.6992 (mtt) cc_final: 0.5697 (tpt) REVERT: A 521 MET cc_start: 0.8152 (mmm) cc_final: 0.7693 (mmm) outliers start: 12 outliers final: 5 residues processed: 60 average time/residue: 0.3956 time to fit residues: 25.8319 Evaluate side-chains 53 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 88 optimal weight: 0.0070 chunk 102 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.109296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.074061 restraints weight = 12737.972| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.13 r_work: 0.2886 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7852 Z= 0.136 Angle : 0.826 30.728 10711 Z= 0.331 Chirality : 0.041 0.132 1306 Planarity : 0.004 0.045 1335 Dihedral : 7.656 77.449 1416 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.61 % Allowed : 10.19 % Favored : 88.20 % 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: 1.70 (0.27), residues: 1016 helix: 2.17 (0.23), residues: 485 sheet: 0.04 (0.37), residues: 175 loop : 0.36 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 366 TYR 0.016 0.001 TYR A 931 PHE 0.012 0.001 PHE A1154 TRP 0.009 0.001 TRP A 253 HIS 0.003 0.001 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7851) covalent geometry : angle 0.82610 (10711) hydrogen bonds : bond 0.03649 ( 467) hydrogen bonds : angle 4.49632 ( 1317) Misc. bond : bond 0.00012 ( 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 62 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 84 HIS cc_start: 0.7920 (m90) cc_final: 0.7568 (m90) REVERT: A 379 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7821 (mmp-170) REVERT: A 385 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.7721 (p90) REVERT: A 421 MET cc_start: 0.6986 (mtt) cc_final: 0.5702 (tpt) REVERT: A 521 MET cc_start: 0.8197 (mmm) cc_final: 0.7735 (mmm) outliers start: 12 outliers final: 5 residues processed: 60 average time/residue: 0.3497 time to fit residues: 23.0905 Evaluate side-chains 53 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.074224 restraints weight = 12808.822| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.14 r_work: 0.2892 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7852 Z= 0.129 Angle : 0.822 30.668 10711 Z= 0.328 Chirality : 0.040 0.131 1306 Planarity : 0.004 0.044 1335 Dihedral : 7.503 77.668 1416 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.47 % Allowed : 10.86 % Favored : 87.67 % 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: 1.82 (0.27), residues: 1016 helix: 2.24 (0.23), residues: 487 sheet: 0.10 (0.37), residues: 180 loop : 0.47 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 816 TYR 0.015 0.001 TYR A 931 PHE 0.011 0.001 PHE A1154 TRP 0.008 0.001 TRP A 253 HIS 0.003 0.001 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7851) covalent geometry : angle 0.82247 (10711) hydrogen bonds : bond 0.03550 ( 467) hydrogen bonds : angle 4.43602 ( 1317) Misc. bond : bond 0.00003 ( 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 61 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.267 Fit side-chains REVERT: A 84 HIS cc_start: 0.7924 (m90) cc_final: 0.7604 (m90) REVERT: A 385 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.7464 (p90) REVERT: A 521 MET cc_start: 0.8224 (mmm) cc_final: 0.7732 (mmm) REVERT: A 973 MET cc_start: 0.8681 (ttp) cc_final: 0.8449 (ptm) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.3550 time to fit residues: 22.1976 Evaluate side-chains 51 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 44 optimal weight: 0.2980 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.109376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.074271 restraints weight = 12858.480| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.13 r_work: 0.2894 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7852 Z= 0.126 Angle : 0.826 30.664 10711 Z= 0.329 Chirality : 0.040 0.126 1306 Planarity : 0.004 0.044 1335 Dihedral : 7.426 76.936 1416 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.47 % Allowed : 11.80 % Favored : 86.73 % 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: 1.91 (0.27), residues: 1016 helix: 2.32 (0.23), residues: 487 sheet: 0.18 (0.37), residues: 180 loop : 0.48 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 816 TYR 0.015 0.001 TYR A 931 PHE 0.034 0.001 PHE A1123 TRP 0.008 0.001 TRP A 253 HIS 0.003 0.001 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7851) covalent geometry : angle 0.82561 (10711) hydrogen bonds : bond 0.03491 ( 467) hydrogen bonds : angle 4.39357 ( 1317) Misc. bond : bond 0.00006 ( 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 61 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.213 Fit side-chains REVERT: A 84 HIS cc_start: 0.7935 (m90) cc_final: 0.7614 (m90) REVERT: A 178 TYR cc_start: 0.7540 (m-80) cc_final: 0.7172 (m-80) REVERT: A 385 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.7468 (p90) REVERT: A 421 MET cc_start: 0.7061 (mtt) cc_final: 0.5824 (tpt) REVERT: A 521 MET cc_start: 0.8255 (mmm) cc_final: 0.7732 (mmm) REVERT: A 541 LEU cc_start: 0.8323 (mt) cc_final: 0.7812 (pt) REVERT: A 1160 GLU cc_start: 0.8150 (pt0) cc_final: 0.7686 (pp20) outliers start: 11 outliers final: 5 residues processed: 58 average time/residue: 0.3532 time to fit residues: 22.4663 Evaluate side-chains 53 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.108921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073611 restraints weight = 12926.945| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.16 r_work: 0.2882 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7852 Z= 0.136 Angle : 0.824 30.887 10711 Z= 0.329 Chirality : 0.040 0.129 1306 Planarity : 0.004 0.043 1335 Dihedral : 7.427 75.883 1416 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.94 % Allowed : 12.47 % Favored : 86.60 % 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: 1.95 (0.27), residues: 1016 helix: 2.30 (0.23), residues: 489 sheet: 0.34 (0.38), residues: 178 loop : 0.48 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 816 TYR 0.015 0.001 TYR A 931 PHE 0.030 0.001 PHE A1123 TRP 0.009 0.001 TRP A 253 HIS 0.003 0.001 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7851) covalent geometry : angle 0.82378 (10711) hydrogen bonds : bond 0.03544 ( 467) hydrogen bonds : angle 4.39601 ( 1317) Misc. bond : bond 0.00006 ( 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 56 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.271 Fit side-chains REVERT: A 84 HIS cc_start: 0.7926 (m90) cc_final: 0.7642 (m90) REVERT: A 385 HIS cc_start: 0.8619 (OUTLIER) cc_final: 0.7576 (p90) REVERT: A 521 MET cc_start: 0.8239 (mmm) cc_final: 0.7719 (mmm) REVERT: A 541 LEU cc_start: 0.8252 (mt) cc_final: 0.7721 (pt) REVERT: A 719 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8275 (mtm) outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.3469 time to fit residues: 20.3195 Evaluate side-chains 51 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 69 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 95 optimal weight: 0.0060 chunk 49 optimal weight: 50.0000 chunk 24 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.108093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073061 restraints weight = 12804.492| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.16 r_work: 0.2833 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7852 Z= 0.147 Angle : 0.835 31.107 10711 Z= 0.335 Chirality : 0.041 0.128 1306 Planarity : 0.004 0.043 1335 Dihedral : 7.362 77.246 1416 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.07 % Allowed : 12.47 % Favored : 86.46 % 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: 1.98 (0.27), residues: 1016 helix: 2.28 (0.23), residues: 489 sheet: 0.42 (0.38), residues: 177 loop : 0.52 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 816 TYR 0.015 0.001 TYR A 931 PHE 0.033 0.001 PHE A1123 TRP 0.009 0.001 TRP A 253 HIS 0.003 0.001 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7851) covalent geometry : angle 0.83516 (10711) hydrogen bonds : bond 0.03599 ( 467) hydrogen bonds : angle 4.40782 ( 1317) Misc. bond : bond 0.00001 ( 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 55 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.291 Fit side-chains REVERT: A 84 HIS cc_start: 0.7977 (m90) cc_final: 0.7672 (m90) REVERT: A 385 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7458 (p90) REVERT: A 421 MET cc_start: 0.6981 (mtt) cc_final: 0.5697 (tpt) REVERT: A 521 MET cc_start: 0.8155 (mmm) cc_final: 0.7587 (mmm) REVERT: A 541 LEU cc_start: 0.8136 (mt) cc_final: 0.7651 (pt) REVERT: A 719 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8074 (mtm) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 0.3403 time to fit residues: 19.7049 Evaluate side-chains 50 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 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 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.108145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.073118 restraints weight = 12716.194| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.15 r_work: 0.2833 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7852 Z= 0.144 Angle : 0.830 30.965 10711 Z= 0.333 Chirality : 0.041 0.129 1306 Planarity : 0.004 0.042 1335 Dihedral : 7.245 79.897 1416 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.80 % Allowed : 12.47 % Favored : 86.73 % 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: 1.98 (0.27), residues: 1016 helix: 2.29 (0.23), residues: 489 sheet: 0.42 (0.38), residues: 178 loop : 0.52 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 816 TYR 0.015 0.001 TYR A 931 PHE 0.031 0.001 PHE A1123 TRP 0.009 0.001 TRP A 253 HIS 0.002 0.001 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7851) covalent geometry : angle 0.82959 (10711) hydrogen bonds : bond 0.03572 ( 467) hydrogen bonds : angle 4.39563 ( 1317) Misc. bond : bond 0.00012 ( 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 55 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.277 Fit side-chains REVERT: A 84 HIS cc_start: 0.7976 (m90) cc_final: 0.7666 (m90) REVERT: A 385 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.7431 (p90) REVERT: A 421 MET cc_start: 0.6958 (mtt) cc_final: 0.5693 (tpt) REVERT: A 521 MET cc_start: 0.8132 (mmm) cc_final: 0.7558 (mmm) REVERT: A 541 LEU cc_start: 0.8081 (mt) cc_final: 0.7690 (pt) REVERT: A 719 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8068 (mtm) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.3462 time to fit residues: 20.2438 Evaluate side-chains 53 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 87 optimal weight: 0.9980 chunk 49 optimal weight: 50.0000 chunk 81 optimal weight: 0.6980 chunk 100 optimal weight: 0.0670 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 0.0770 chunk 97 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.109316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074163 restraints weight = 12728.012| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.16 r_work: 0.2856 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7852 Z= 0.110 Angle : 0.818 30.464 10711 Z= 0.325 Chirality : 0.040 0.137 1306 Planarity : 0.004 0.042 1335 Dihedral : 7.132 80.675 1416 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.94 % Allowed : 12.73 % Favored : 86.33 % 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: 2.11 (0.27), residues: 1016 helix: 2.39 (0.23), residues: 489 sheet: 0.50 (0.38), residues: 177 loop : 0.56 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 816 TYR 0.015 0.001 TYR A 931 PHE 0.031 0.001 PHE A1123 TRP 0.009 0.001 TRP A 253 HIS 0.002 0.000 HIS A 775 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7851) covalent geometry : angle 0.81759 (10711) hydrogen bonds : bond 0.03345 ( 467) hydrogen bonds : angle 4.30560 ( 1317) Misc. bond : bond 0.00012 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2904.22 seconds wall clock time: 50 minutes 2.77 seconds (3002.77 seconds total)