Starting phenix.real_space_refine on Tue Apr 29 19:13:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n72_24217/04_2025/7n72_24217_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n72_24217/04_2025/7n72_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_24217/04_2025/7n72_24217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n72_24217/04_2025/7n72_24217.map" model { file = "/net/cci-nas-00/data/ceres_data/7n72_24217/04_2025/7n72_24217_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n72_24217/04_2025/7n72_24217_trim.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'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': 17} 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: 5.63, per 1000 atoms: 0.73 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: 2.34 Conformation dependent library (CDL) restraints added in 981.0 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: 1.04 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: 3.34 Time building geometry restraints manager: 2.74 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.130 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- 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 (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: -0.87 (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 TRP 0.010 0.002 TRP A1166 HIS 0.014 0.002 HIS A 84 PHE 0.011 0.002 PHE A1154 TYR 0.016 0.002 TYR A 931 ARG 0.030 0.002 ARG A 444 Details of bonding type rmsd hydrogen bonds : bond 0.14681 ( 467) hydrogen bonds : angle 6.32723 ( 1317) covalent geometry : bond 0.00714 ( 7851) covalent geometry : angle 1.34534 (10711) 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 : 0.762 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: 1.2597 time to fit residues: 105.8491 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 : 0.832 ------------------------------------------------------------------------------- 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: 0.6980 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 40.0000 chunk 60 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3625 r_free = 0.3625 target = 0.110336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074978 restraints weight = 12654.935| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.13 r_work: 0.2871 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7852 Z= 0.131 Angle : 0.846 31.084 10711 Z= 0.347 Chirality : 0.041 0.136 1306 Planarity : 0.005 0.056 1335 Dihedral : 8.708 80.049 1416 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.94 % Allowed : 7.37 % Favored : 91.69 % 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: 0.74 (0.26), residues: 1016 helix: 1.24 (0.23), residues: 486 sheet: -0.23 (0.38), residues: 169 loop : 0.00 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 253 HIS 0.004 0.001 HIS A 831 PHE 0.012 0.001 PHE A1154 TYR 0.017 0.001 TYR A 931 ARG 0.010 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 467) hydrogen bonds : angle 4.83399 ( 1317) covalent geometry : bond 0.00294 ( 7851) covalent geometry : angle 0.84626 (10711) Misc. bond : bond 0.00098 ( 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 : 0.775 Fit side-chains revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7887 (m-80) cc_final: 0.7233 (m-80) REVERT: A 421 MET cc_start: 0.6961 (mtt) cc_final: 0.5733 (tpt) REVERT: A 521 MET cc_start: 0.7981 (mmm) cc_final: 0.7667 (mmm) REVERT: A 955 ASP cc_start: 0.8961 (m-30) cc_final: 0.8626 (m-30) outliers start: 7 outliers final: 1 residues processed: 57 average time/residue: 0.8845 time to fit residues: 55.1093 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 : 0.782 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.108821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.073278 restraints weight = 12853.048| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.14 r_work: 0.2842 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7852 Z= 0.176 Angle : 0.849 31.090 10711 Z= 0.345 Chirality : 0.042 0.139 1306 Planarity : 0.005 0.044 1335 Dihedral : 8.220 76.036 1416 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.47 % Allowed : 7.77 % Favored : 90.75 % 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: 1.23 (0.27), residues: 1016 helix: 1.69 (0.23), residues: 485 sheet: 0.07 (0.38), residues: 165 loop : 0.11 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.003 0.001 HIS A 775 PHE 0.013 0.001 PHE A1154 TYR 0.017 0.001 TYR A 931 ARG 0.005 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 467) hydrogen bonds : angle 4.68812 ( 1317) covalent geometry : bond 0.00408 ( 7851) covalent geometry : angle 0.84874 (10711) Misc. bond : bond 0.00015 ( 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 : 0.901 Fit side-chains REVERT: A 84 HIS cc_start: 0.7931 (m90) cc_final: 0.7551 (m90) REVERT: A 379 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7904 (mmp-170) REVERT: A 421 MET cc_start: 0.7091 (mtt) cc_final: 0.5818 (tpt) REVERT: A 521 MET cc_start: 0.8141 (mmm) cc_final: 0.7683 (mmm) outliers start: 11 outliers final: 4 residues processed: 57 average time/residue: 0.8961 time to fit residues: 56.0685 Evaluate side-chains 50 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 787 LEU 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 33 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 57 optimal weight: 0.4980 chunk 27 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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** 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 = 0.3639 r_free = 0.3639 target = 0.110840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.075702 restraints weight = 12698.178| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.14 r_work: 0.2891 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7852 Z= 0.104 Angle : 0.810 30.096 10711 Z= 0.322 Chirality : 0.040 0.135 1306 Planarity : 0.004 0.045 1335 Dihedral : 7.638 78.930 1416 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.34 % Allowed : 9.65 % Favored : 89.01 % 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: 1.56 (0.27), residues: 1016 helix: 2.07 (0.23), residues: 487 sheet: -0.08 (0.37), residues: 175 loop : 0.28 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 253 HIS 0.003 0.000 HIS A 775 PHE 0.011 0.001 PHE A1154 TYR 0.015 0.001 TYR A 931 ARG 0.003 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 467) hydrogen bonds : angle 4.44987 ( 1317) covalent geometry : bond 0.00233 ( 7851) covalent geometry : angle 0.81014 (10711) Misc. bond : bond 0.00000 ( 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 63 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 84 HIS cc_start: 0.7883 (m90) cc_final: 0.7557 (m90) REVERT: A 178 TYR cc_start: 0.7751 (m-80) cc_final: 0.7242 (m-80) REVERT: A 385 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.7444 (p90) REVERT: A 421 MET cc_start: 0.7002 (mtt) cc_final: 0.5688 (tpt) REVERT: A 521 MET cc_start: 0.8192 (mmm) cc_final: 0.7714 (mmm) REVERT: A 1160 GLU cc_start: 0.8194 (pt0) cc_final: 0.7748 (pp20) outliers start: 10 outliers final: 4 residues processed: 59 average time/residue: 0.8837 time to fit residues: 57.1701 Evaluate side-chains 52 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 385 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 102 optimal weight: 0.0980 chunk 67 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 4 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.110713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.075702 restraints weight = 12701.451| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.14 r_work: 0.2893 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7852 Z= 0.104 Angle : 0.809 30.244 10711 Z= 0.320 Chirality : 0.040 0.136 1306 Planarity : 0.004 0.045 1335 Dihedral : 7.379 76.901 1416 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.21 % Allowed : 10.59 % 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 (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: 1.84 (0.27), residues: 1016 helix: 2.30 (0.23), residues: 487 sheet: 0.03 (0.37), residues: 180 loop : 0.44 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 253 HIS 0.003 0.000 HIS A 775 PHE 0.011 0.001 PHE A1154 TYR 0.014 0.001 TYR A 931 ARG 0.002 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 467) hydrogen bonds : angle 4.34659 ( 1317) covalent geometry : bond 0.00232 ( 7851) covalent geometry : angle 0.80883 (10711) Misc. bond : bond 0.00002 ( 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 61 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 84 HIS cc_start: 0.7884 (m90) cc_final: 0.7573 (m90) REVERT: A 174 GLN cc_start: 0.8279 (tt0) cc_final: 0.7714 (tm-30) REVERT: A 178 TYR cc_start: 0.7547 (m-80) cc_final: 0.7095 (m-80) REVERT: A 385 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.7774 (p90) REVERT: A 421 MET cc_start: 0.6993 (mtt) cc_final: 0.5696 (tpt) REVERT: A 521 MET cc_start: 0.8241 (mmm) cc_final: 0.7857 (mmm) REVERT: A 1160 GLU cc_start: 0.8152 (pt0) cc_final: 0.7775 (pp20) outliers start: 9 outliers final: 4 residues processed: 59 average time/residue: 1.1364 time to fit residues: 72.5710 Evaluate side-chains 53 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 55 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 179 GLN A1122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.108998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.073723 restraints weight = 12719.379| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.14 r_work: 0.2882 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7852 Z= 0.157 Angle : 0.832 31.192 10711 Z= 0.333 Chirality : 0.041 0.139 1306 Planarity : 0.004 0.045 1335 Dihedral : 7.485 74.875 1416 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.34 % Allowed : 10.32 % Favored : 88.34 % 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: 1.85 (0.27), residues: 1016 helix: 2.25 (0.23), residues: 487 sheet: 0.12 (0.37), residues: 180 loop : 0.48 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 253 HIS 0.003 0.001 HIS A 197 PHE 0.011 0.001 PHE A1154 TYR 0.015 0.001 TYR A 931 ARG 0.002 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 467) hydrogen bonds : angle 4.43414 ( 1317) covalent geometry : bond 0.00365 ( 7851) covalent geometry : angle 0.83207 (10711) Misc. bond : bond 0.00013 ( 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 62 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.879 Fit side-chains REVERT: A 84 HIS cc_start: 0.7915 (m90) cc_final: 0.7618 (m90) REVERT: A 174 GLN cc_start: 0.8202 (tt0) cc_final: 0.7567 (tm-30) REVERT: A 178 TYR cc_start: 0.7736 (m-80) cc_final: 0.7071 (m-80) REVERT: A 385 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.7472 (p90) REVERT: A 521 MET cc_start: 0.8293 (mmm) cc_final: 0.7758 (mmm) REVERT: A 1123 PHE cc_start: 0.8548 (t80) cc_final: 0.8335 (t80) outliers start: 10 outliers final: 5 residues processed: 59 average time/residue: 0.7716 time to fit residues: 50.5015 Evaluate side-chains 52 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.110139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.075056 restraints weight = 12786.097| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.15 r_work: 0.2880 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7852 Z= 0.110 Angle : 0.815 30.236 10711 Z= 0.323 Chirality : 0.040 0.129 1306 Planarity : 0.004 0.044 1335 Dihedral : 7.240 75.775 1416 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.07 % Allowed : 11.13 % Favored : 87.80 % 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: 1.99 (0.27), residues: 1016 helix: 2.38 (0.23), residues: 487 sheet: 0.15 (0.37), residues: 180 loop : 0.56 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 253 HIS 0.003 0.000 HIS A 775 PHE 0.011 0.001 PHE A1154 TYR 0.015 0.001 TYR A 931 ARG 0.001 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 467) hydrogen bonds : angle 4.35997 ( 1317) covalent geometry : bond 0.00247 ( 7851) covalent geometry : angle 0.81497 (10711) Misc. bond : bond 0.00001 ( 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 60 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.984 Fit side-chains REVERT: A 84 HIS cc_start: 0.7936 (m90) cc_final: 0.7628 (m90) REVERT: A 174 GLN cc_start: 0.8321 (tt0) cc_final: 0.7683 (tm-30) REVERT: A 178 TYR cc_start: 0.7825 (m-80) cc_final: 0.7200 (m-80) REVERT: A 385 HIS cc_start: 0.8659 (OUTLIER) cc_final: 0.7556 (p90) REVERT: A 421 MET cc_start: 0.7070 (mtt) cc_final: 0.5832 (tpt) REVERT: A 521 MET cc_start: 0.8248 (mmm) cc_final: 0.7857 (mmm) REVERT: A 541 LEU cc_start: 0.8318 (mt) cc_final: 0.7780 (pt) REVERT: A 1160 GLU cc_start: 0.8145 (pt0) cc_final: 0.7737 (pp20) outliers start: 8 outliers final: 4 residues processed: 57 average time/residue: 0.8307 time to fit residues: 52.7353 Evaluate side-chains 54 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 84 optimal weight: 0.0370 chunk 48 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- 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** A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.109651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.074420 restraints weight = 12808.737| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.15 r_work: 0.2867 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7852 Z= 0.126 Angle : 0.825 30.733 10711 Z= 0.328 Chirality : 0.040 0.131 1306 Planarity : 0.004 0.044 1335 Dihedral : 7.170 75.391 1416 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.21 % Allowed : 11.53 % Favored : 87.27 % 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: 2.05 (0.27), residues: 1016 helix: 2.38 (0.23), residues: 489 sheet: 0.31 (0.38), residues: 178 loop : 0.57 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 253 HIS 0.002 0.001 HIS A 775 PHE 0.036 0.001 PHE A1123 TYR 0.015 0.001 TYR A 931 ARG 0.002 0.000 ARG A 816 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 467) hydrogen bonds : angle 4.37195 ( 1317) covalent geometry : bond 0.00290 ( 7851) covalent geometry : angle 0.82524 (10711) Misc. bond : bond 0.00003 ( 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 58 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.887 Fit side-chains REVERT: A 84 HIS cc_start: 0.7978 (m90) cc_final: 0.7684 (m90) REVERT: A 174 GLN cc_start: 0.8182 (tt0) cc_final: 0.7548 (tm-30) REVERT: A 178 TYR cc_start: 0.7924 (m-80) cc_final: 0.7256 (m-80) REVERT: A 521 MET cc_start: 0.8286 (mmm) cc_final: 0.7882 (mmm) REVERT: A 541 LEU cc_start: 0.8212 (mt) cc_final: 0.7639 (pp) REVERT: A 1160 GLU cc_start: 0.8181 (pt0) cc_final: 0.7749 (pp20) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.8246 time to fit residues: 51.0858 Evaluate side-chains 52 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 46 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.109096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.073813 restraints weight = 13017.240| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.17 r_work: 0.2886 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7852 Z= 0.142 Angle : 0.828 30.971 10711 Z= 0.331 Chirality : 0.040 0.129 1306 Planarity : 0.004 0.044 1335 Dihedral : 7.242 77.388 1416 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.54 % Allowed : 11.93 % Favored : 87.53 % 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: 2.04 (0.27), residues: 1016 helix: 2.32 (0.23), residues: 490 sheet: 0.37 (0.38), residues: 178 loop : 0.61 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 253 HIS 0.002 0.001 HIS A 775 PHE 0.029 0.001 PHE A1123 TYR 0.015 0.001 TYR A 931 ARG 0.002 0.000 ARG A 816 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 467) hydrogen bonds : angle 4.41000 ( 1317) covalent geometry : bond 0.00328 ( 7851) covalent geometry : angle 0.82820 (10711) Misc. bond : bond 0.00007 ( 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 54 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.837 Fit side-chains REVERT: A 84 HIS cc_start: 0.8006 (m90) cc_final: 0.7726 (m90) REVERT: A 174 GLN cc_start: 0.8204 (tt0) cc_final: 0.7541 (tm-30) REVERT: A 178 TYR cc_start: 0.7919 (m-80) cc_final: 0.7192 (m-80) REVERT: A 421 MET cc_start: 0.7133 (mtt) cc_final: 0.5770 (tpt) REVERT: A 521 MET cc_start: 0.8305 (mmm) cc_final: 0.7893 (mmm) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.8178 time to fit residues: 48.0502 Evaluate side-chains 50 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 5 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 50.0000 chunk 75 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.108509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.073630 restraints weight = 12771.741| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.15 r_work: 0.2843 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2140 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= 0.142 Angle : 0.836 31.035 10711 Z= 0.334 Chirality : 0.041 0.124 1306 Planarity : 0.004 0.043 1335 Dihedral : 7.239 80.689 1416 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.54 % Allowed : 12.06 % Favored : 87.40 % 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: 2.03 (0.27), residues: 1016 helix: 2.35 (0.23), residues: 488 sheet: 0.45 (0.38), residues: 178 loop : 0.50 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 253 HIS 0.002 0.001 HIS A 775 PHE 0.032 0.001 PHE A1123 TYR 0.015 0.001 TYR A 931 ARG 0.002 0.000 ARG A 816 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 467) hydrogen bonds : angle 4.39320 ( 1317) covalent geometry : bond 0.00330 ( 7851) covalent geometry : angle 0.83584 (10711) Misc. bond : bond 0.00010 ( 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 53 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.812 Fit side-chains REVERT: A 84 HIS cc_start: 0.7997 (m90) cc_final: 0.7719 (m90) REVERT: A 178 TYR cc_start: 0.7770 (m-80) cc_final: 0.7499 (m-80) REVERT: A 385 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.7511 (p90) REVERT: A 421 MET cc_start: 0.6957 (mtt) cc_final: 0.5690 (tpt) REVERT: A 521 MET cc_start: 0.8210 (mmm) cc_final: 0.7728 (mmm) REVERT: A 541 LEU cc_start: 0.8177 (mp) cc_final: 0.7668 (pp) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.8231 time to fit residues: 47.4185 Evaluate side-chains 51 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 HIS 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 40 optimal weight: 0.6980 chunk 66 optimal weight: 0.0670 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 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 = 0.3611 r_free = 0.3611 target = 0.109311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.074450 restraints weight = 12694.602| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.15 r_work: 0.2863 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7852 Z= 0.116 Angle : 0.816 30.604 10711 Z= 0.324 Chirality : 0.040 0.153 1306 Planarity : 0.004 0.043 1335 Dihedral : 7.118 81.628 1416 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.80 % Allowed : 11.66 % Favored : 87.53 % 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: 2.16 (0.27), residues: 1016 helix: 2.42 (0.23), residues: 490 sheet: 0.53 (0.39), residues: 177 loop : 0.60 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 253 HIS 0.002 0.000 HIS A 775 PHE 0.031 0.001 PHE A1123 TYR 0.015 0.001 TYR A 931 ARG 0.001 0.000 ARG A 816 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 467) hydrogen bonds : angle 4.30740 ( 1317) covalent geometry : bond 0.00263 ( 7851) covalent geometry : angle 0.81594 (10711) Misc. bond : bond 0.00004 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6478.52 seconds wall clock time: 112 minutes 55.96 seconds (6775.96 seconds total)