Starting phenix.real_space_refine on Wed Feb 12 01:11:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij5_60616/02_2025/9ij5_60616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij5_60616/02_2025/9ij5_60616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ij5_60616/02_2025/9ij5_60616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij5_60616/02_2025/9ij5_60616.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij5_60616/02_2025/9ij5_60616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij5_60616/02_2025/9ij5_60616.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 4368 2.51 5 N 1236 2.21 5 O 1439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7139 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6057 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 717} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 550 Classifications: {'RNA': 26} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 24} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 531 Classifications: {'RNA': 25} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 22} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.40, per 1000 atoms: 0.62 Number of scatterers: 7139 At special positions: 0 Unit cell: (77.52, 86.64, 106.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 51 15.00 Mg 1 11.99 O 1439 8.00 N 1236 7.00 C 4368 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=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 709.3 milliseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 8 sheets defined 33.2% alpha, 24.9% beta 23 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 388 through 399 Processing helix chain 'A' and resid 402 through 412 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 508 through 520 removed outlier: 3.666A pdb=" N MET A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 540 Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 612 through 631 removed outlier: 3.790A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 646 through 661 removed outlier: 3.771A pdb=" N TYR A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 686 removed outlier: 3.970A pdb=" N TYR A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 723 removed outlier: 4.127A pdb=" N VAL A 711 " --> pdb=" O ARG A 707 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 723 " --> pdb=" O MET A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 801 removed outlier: 4.092A pdb=" N LEU A 788 " --> pdb=" O ASP A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 818 No H-bonds generated for 'chain 'A' and resid 816 through 818' Processing helix chain 'A' and resid 819 through 826 Processing helix chain 'A' and resid 826 through 835 Processing helix chain 'A' and resid 836 through 838 No H-bonds generated for 'chain 'A' and resid 836 through 838' Processing helix chain 'A' and resid 916 through 928 Processing helix chain 'A' and resid 939 through 955 Processing helix chain 'A' and resid 961 through 965 Processing sheet with id=AA1, first strand: chain 'A' and resid 769 through 774 removed outlier: 3.726A pdb=" N ASP A 743 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL A 739 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET A 845 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN A 909 " --> pdb=" O MET A 845 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 847 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 887 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL A 885 " --> pdb=" O CYS A 906 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER A 223 " --> pdb=" O ALA A 861 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 859 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.773A pdb=" N PHE A 341 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 384 " --> pdb=" O MET A 498 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N MET A 498 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASP A 386 " --> pdb=" O SER A 496 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N SER A 496 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 499 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE A 415 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272 removed outlier: 6.321A pdb=" N HIS A 242 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU A 306 " --> pdb=" O HIS A 242 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR A 244 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE A 304 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N SER A 246 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE A 302 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA7, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AA8, first strand: chain 'A' and resid 638 through 641 removed outlier: 6.302A pdb=" N ALA A 605 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE A 670 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE A 607 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 667 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A 697 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS A 669 " --> pdb=" O ILE A 697 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 2.26 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: 1805 1.33 - 1.46: 1901 1.46 - 1.58: 3524 1.58 - 1.70: 101 1.70 - 1.83: 69 Bond restraints: 7400 Sorted by residual: bond pdb=" C ALA A 862 " pdb=" N PRO A 863 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.08e-02 8.57e+03 1.01e+01 bond pdb=" CB PRO A 221 " pdb=" CG PRO A 221 " ideal model delta sigma weight residual 1.492 1.642 -0.150 5.00e-02 4.00e+02 9.02e+00 bond pdb=" CG GLN A 830 " pdb=" CD GLN A 830 " ideal model delta sigma weight residual 1.516 1.445 0.071 2.50e-02 1.60e+03 8.01e+00 bond pdb=" CG LEU A 372 " pdb=" CD2 LEU A 372 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.74e+00 bond pdb=" CB LYS A 290 " pdb=" CG LYS A 290 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.81e+00 ... (remaining 7395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 9935 2.91 - 5.82: 279 5.82 - 8.72: 32 8.72 - 11.63: 13 11.63 - 14.54: 4 Bond angle restraints: 10263 Sorted by residual: angle pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" CD PRO A 221 " ideal model delta sigma weight residual 112.00 97.46 14.54 1.40e+00 5.10e-01 1.08e+02 angle pdb=" CA MET A 329 " pdb=" CB MET A 329 " pdb=" CG MET A 329 " ideal model delta sigma weight residual 114.10 126.01 -11.91 2.00e+00 2.50e-01 3.55e+01 angle pdb=" C ILE A 782 " pdb=" CA ILE A 782 " pdb=" CB ILE A 782 " ideal model delta sigma weight residual 111.29 120.47 -9.18 1.64e+00 3.72e-01 3.13e+01 angle pdb=" CA LYS A 290 " pdb=" CB LYS A 290 " pdb=" CG LYS A 290 " ideal model delta sigma weight residual 114.10 125.05 -10.95 2.00e+00 2.50e-01 3.00e+01 angle pdb=" CA PRO A 468 " pdb=" N PRO A 468 " pdb=" CD PRO A 468 " ideal model delta sigma weight residual 112.00 104.72 7.28 1.40e+00 5.10e-01 2.71e+01 ... (remaining 10258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3697 17.83 - 35.66: 551 35.66 - 53.48: 169 53.48 - 71.31: 83 71.31 - 89.14: 21 Dihedral angle restraints: 4521 sinusoidal: 2311 harmonic: 2210 Sorted by residual: dihedral pdb=" CA ILE A 231 " pdb=" C ILE A 231 " pdb=" N GLN A 232 " pdb=" CA GLN A 232 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA MET A 329 " pdb=" C MET A 329 " pdb=" N LYS A 330 " pdb=" CA LYS A 330 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" C ILE A 782 " pdb=" N ILE A 782 " pdb=" CA ILE A 782 " pdb=" CB ILE A 782 " ideal model delta harmonic sigma weight residual -122.00 -132.96 10.96 0 2.50e+00 1.60e-01 1.92e+01 ... (remaining 4518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1016 0.086 - 0.173: 174 0.173 - 0.259: 10 0.259 - 0.346: 2 0.346 - 0.432: 2 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CB VAL A 791 " pdb=" CA VAL A 791 " pdb=" CG1 VAL A 791 " pdb=" CG2 VAL A 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CB ILE A 854 " pdb=" CA ILE A 854 " pdb=" CG1 ILE A 854 " pdb=" CG2 ILE A 854 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CB ILE A 229 " pdb=" CA ILE A 229 " pdb=" CG1 ILE A 229 " pdb=" CG2 ILE A 229 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1201 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 220 " 0.116 5.00e-02 4.00e+02 1.63e-01 4.25e+01 pdb=" N PRO A 221 " -0.281 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 652 " -0.209 9.50e-02 1.11e+02 9.44e-02 7.16e+00 pdb=" NE ARG A 652 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 652 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 652 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 652 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 467 " -0.044 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO A 468 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.036 5.00e-02 4.00e+02 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1641 2.79 - 3.32: 5991 3.32 - 3.85: 13389 3.85 - 4.37: 15385 4.37 - 4.90: 24752 Nonbonded interactions: 61158 Sorted by model distance: nonbonded pdb=" O THR A 649 " pdb=" OG1 THR A 653 " model vdw 2.267 3.040 nonbonded pdb=" O SER A 544 " pdb=" OG1 THR A 548 " model vdw 2.300 3.040 nonbonded pdb=" O PRO A 312 " pdb=" OH TYR A 321 " model vdw 2.321 3.040 nonbonded pdb=" ND2 ASN A 322 " pdb=" O3' C C 12 " model vdw 2.340 3.120 nonbonded pdb=" O GLY A 338 " pdb=" ND2 ASN A 422 " model vdw 2.350 3.120 ... (remaining 61153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.180 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.550 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 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 : 0.008 0.150 7400 Z= 0.498 Angle : 1.161 14.538 10263 Z= 0.607 Chirality : 0.064 0.432 1204 Planarity : 0.010 0.163 1111 Dihedral : 19.966 89.140 3091 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.02 % Allowed : 31.92 % Favored : 67.06 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.70 % 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: -2.72 (0.27), residues: 751 helix: -1.94 (0.28), residues: 215 sheet: -0.83 (0.40), residues: 167 loop : -2.16 (0.28), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP A 639 HIS 0.013 0.002 HIS A 946 PHE 0.032 0.004 PHE A 838 TYR 0.018 0.003 TYR A 361 ARG 0.023 0.001 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.617 Fit side-chains REVERT: A 769 TRP cc_start: 0.7081 (m100) cc_final: 0.6821 (m100) REVERT: A 845 MET cc_start: 0.8302 (ttt) cc_final: 0.7968 (ttt) outliers start: 7 outliers final: 3 residues processed: 105 average time/residue: 0.9495 time to fit residues: 106.8675 Evaluate side-chains 95 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 936 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS A 555 HIS ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.211965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.176942 restraints weight = 8355.818| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.13 r_work: 0.4181 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4069 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7400 Z= 0.190 Angle : 0.615 7.731 10263 Z= 0.318 Chirality : 0.043 0.183 1204 Planarity : 0.005 0.079 1111 Dihedral : 17.624 82.068 1590 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.69 % Allowed : 31.48 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.91 (0.28), residues: 751 helix: -0.55 (0.32), residues: 221 sheet: -0.90 (0.38), residues: 176 loop : -1.89 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 639 HIS 0.003 0.001 HIS A 903 PHE 0.019 0.002 PHE A 325 TYR 0.011 0.001 TYR A 241 ARG 0.009 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.689 Fit side-chains REVERT: A 327 ARG cc_start: 0.5320 (OUTLIER) cc_final: 0.4822 (mtt-85) REVERT: A 330 LYS cc_start: 0.6341 (OUTLIER) cc_final: 0.5986 (tptt) REVERT: A 348 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6723 (pmm) REVERT: A 456 LYS cc_start: 0.6687 (OUTLIER) cc_final: 0.5267 (tptt) REVERT: A 473 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6992 (ptp90) REVERT: A 505 MET cc_start: 0.7265 (ttt) cc_final: 0.6969 (ttt) REVERT: A 736 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.6206 (mm110) REVERT: A 777 MET cc_start: 0.2876 (mmp) cc_final: 0.2572 (mmt) REVERT: A 801 ASN cc_start: 0.5504 (t0) cc_final: 0.5166 (t0) REVERT: A 845 MET cc_start: 0.8484 (ttt) cc_final: 0.8094 (ttt) outliers start: 32 outliers final: 7 residues processed: 119 average time/residue: 0.9835 time to fit residues: 124.9494 Evaluate side-chains 101 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 910 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS A 559 HIS A 746 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.195302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.157364 restraints weight = 8467.456| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.25 r_work: 0.3865 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 7400 Z= 0.474 Angle : 0.821 7.872 10263 Z= 0.420 Chirality : 0.051 0.241 1204 Planarity : 0.006 0.041 1111 Dihedral : 17.560 81.038 1580 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 6.73 % Allowed : 28.99 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.94 (0.28), residues: 751 helix: -0.44 (0.32), residues: 218 sheet: -1.02 (0.38), residues: 175 loop : -1.93 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 932 HIS 0.012 0.002 HIS A 946 PHE 0.034 0.003 PHE A 950 TYR 0.017 0.003 TYR A 361 ARG 0.007 0.001 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 100 time to evaluate : 0.692 Fit side-chains REVERT: A 231 ILE cc_start: 0.3814 (OUTLIER) cc_final: 0.3489 (mt) REVERT: A 290 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7755 (mppt) REVERT: A 305 GLN cc_start: 0.7184 (tp40) cc_final: 0.6589 (tp40) REVERT: A 327 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.5017 (mtt-85) REVERT: A 329 MET cc_start: 0.8295 (tmt) cc_final: 0.7934 (tmt) REVERT: A 486 LYS cc_start: 0.5409 (OUTLIER) cc_final: 0.4073 (ttpt) REVERT: A 503 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6206 (pm20) REVERT: A 505 MET cc_start: 0.7242 (ttt) cc_final: 0.6886 (ttt) REVERT: A 512 MET cc_start: 0.7589 (mmm) cc_final: 0.7189 (mmm) REVERT: A 646 ARG cc_start: 0.5641 (mtm110) cc_final: 0.5098 (mtm110) REVERT: A 666 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6532 (tpp) REVERT: A 670 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7124 (mp) REVERT: A 801 ASN cc_start: 0.5547 (t0) cc_final: 0.4945 (t0) outliers start: 46 outliers final: 22 residues processed: 131 average time/residue: 0.8717 time to fit residues: 122.9914 Evaluate side-chains 113 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS A 385 ASN A 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.212209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.179125 restraints weight = 8572.122| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.02 r_work: 0.4270 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4165 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7400 Z= 0.174 Angle : 0.599 7.817 10263 Z= 0.310 Chirality : 0.044 0.216 1204 Planarity : 0.004 0.038 1111 Dihedral : 17.518 84.551 1580 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.27 % Allowed : 31.19 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.33 (0.29), residues: 751 helix: 0.40 (0.34), residues: 214 sheet: -0.86 (0.39), residues: 162 loop : -1.66 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 639 HIS 0.004 0.001 HIS A 892 PHE 0.014 0.002 PHE A 341 TYR 0.012 0.001 TYR A 770 ARG 0.004 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.575 Fit side-chains REVERT: A 230 LYS cc_start: 0.4334 (OUTLIER) cc_final: 0.2255 (ptpp) REVERT: A 231 ILE cc_start: 0.2686 (OUTLIER) cc_final: 0.2143 (mt) REVERT: A 261 ASP cc_start: 0.5521 (m-30) cc_final: 0.5318 (m-30) REVERT: A 348 MET cc_start: 0.7294 (pmm) cc_final: 0.6909 (pmm) REVERT: A 456 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6278 (tmmt) REVERT: A 670 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7278 (mp) REVERT: A 682 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6638 (mp) REVERT: A 777 MET cc_start: 0.2925 (mmp) cc_final: 0.2506 (mmt) REVERT: A 801 ASN cc_start: 0.5486 (t0) cc_final: 0.4802 (t0) outliers start: 36 outliers final: 13 residues processed: 129 average time/residue: 0.9149 time to fit residues: 126.8099 Evaluate side-chains 109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 22 optimal weight: 0.0030 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.210262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.176997 restraints weight = 8405.509| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 1.98 r_work: 0.4246 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4138 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7400 Z= 0.213 Angle : 0.629 6.975 10263 Z= 0.321 Chirality : 0.044 0.183 1204 Planarity : 0.004 0.041 1111 Dihedral : 17.425 82.988 1580 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.73 % Allowed : 30.89 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.15 (0.30), residues: 751 helix: 0.59 (0.35), residues: 216 sheet: -0.80 (0.39), residues: 165 loop : -1.56 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 639 HIS 0.006 0.001 HIS A 946 PHE 0.016 0.002 PHE A 950 TYR 0.010 0.001 TYR A 770 ARG 0.010 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.740 Fit side-chains REVERT: A 230 LYS cc_start: 0.4452 (OUTLIER) cc_final: 0.3433 (ptpp) REVERT: A 231 ILE cc_start: 0.2139 (OUTLIER) cc_final: 0.1888 (mt) REVERT: A 288 GLU cc_start: 0.7056 (mp0) cc_final: 0.6626 (tp30) REVERT: A 305 GLN cc_start: 0.7252 (tp40) cc_final: 0.6804 (tp40) REVERT: A 329 MET cc_start: 0.7339 (tmm) cc_final: 0.7121 (tmt) REVERT: A 348 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6813 (pmm) REVERT: A 503 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5918 (pm20) REVERT: A 670 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7282 (mp) REVERT: A 736 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6577 (mm110) REVERT: A 777 MET cc_start: 0.3279 (mmp) cc_final: 0.3008 (mmt) REVERT: A 801 ASN cc_start: 0.5752 (t0) cc_final: 0.5208 (t0) REVERT: A 852 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6472 (ttmm) REVERT: A 878 THR cc_start: 0.8231 (m) cc_final: 0.7927 (m) outliers start: 46 outliers final: 22 residues processed: 133 average time/residue: 0.9462 time to fit residues: 134.8244 Evaluate side-chains 125 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN A 353 HIS A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.199861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.164317 restraints weight = 8418.518| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.06 r_work: 0.4022 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7400 Z= 0.385 Angle : 0.761 6.997 10263 Z= 0.387 Chirality : 0.049 0.220 1204 Planarity : 0.005 0.071 1111 Dihedral : 17.467 82.533 1580 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 6.44 % Allowed : 31.33 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.48 (0.29), residues: 751 helix: 0.29 (0.34), residues: 215 sheet: -1.03 (0.37), residues: 178 loop : -1.72 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 639 HIS 0.006 0.001 HIS A 903 PHE 0.026 0.003 PHE A 950 TYR 0.014 0.002 TYR A 888 ARG 0.009 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 0.718 Fit side-chains REVERT: A 230 LYS cc_start: 0.5193 (OUTLIER) cc_final: 0.3299 (ptpp) REVERT: A 231 ILE cc_start: 0.3129 (OUTLIER) cc_final: 0.2828 (mt) REVERT: A 254 MET cc_start: 0.5981 (pmm) cc_final: 0.5757 (pmt) REVERT: A 305 GLN cc_start: 0.7296 (tp40) cc_final: 0.6705 (tp40) REVERT: A 503 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.6047 (pm20) REVERT: A 670 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7092 (mp) REVERT: A 801 ASN cc_start: 0.5697 (t0) cc_final: 0.5074 (t0) REVERT: A 852 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.6308 (ttmm) REVERT: A 878 THR cc_start: 0.8519 (m) cc_final: 0.8286 (m) outliers start: 44 outliers final: 22 residues processed: 136 average time/residue: 0.9154 time to fit residues: 133.6187 Evaluate side-chains 120 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS ** A 457 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 = 0.4476 r_free = 0.4476 target = 0.206086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.171537 restraints weight = 8332.588| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.05 r_work: 0.4141 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7400 Z= 0.217 Angle : 0.653 7.609 10263 Z= 0.333 Chirality : 0.044 0.198 1204 Planarity : 0.005 0.046 1111 Dihedral : 17.412 84.505 1580 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.83 % Allowed : 34.41 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.30), residues: 751 helix: 0.55 (0.34), residues: 215 sheet: -0.98 (0.38), residues: 171 loop : -1.55 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 639 HIS 0.006 0.001 HIS A 353 PHE 0.017 0.002 PHE A 950 TYR 0.012 0.001 TYR A 770 ARG 0.011 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.690 Fit side-chains REVERT: A 230 LYS cc_start: 0.4530 (OUTLIER) cc_final: 0.2418 (ptpp) REVERT: A 231 ILE cc_start: 0.2632 (OUTLIER) cc_final: 0.2391 (mt) REVERT: A 288 GLU cc_start: 0.7217 (mp0) cc_final: 0.6813 (tp30) REVERT: A 305 GLN cc_start: 0.7220 (tp40) cc_final: 0.6650 (tp40) REVERT: A 670 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7225 (mp) REVERT: A 682 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6570 (mp) REVERT: A 777 MET cc_start: 0.2565 (mmp) cc_final: 0.2050 (mmt) REVERT: A 801 ASN cc_start: 0.5897 (t0) cc_final: 0.5277 (t0) REVERT: A 852 LYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6288 (ttmm) REVERT: A 878 THR cc_start: 0.8277 (m) cc_final: 0.7998 (m) REVERT: A 942 CYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8041 (m) outliers start: 33 outliers final: 20 residues processed: 125 average time/residue: 0.8799 time to fit residues: 118.3661 Evaluate side-chains 123 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 942 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN A 840 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.204316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.169188 restraints weight = 8465.493| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.08 r_work: 0.4076 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7400 Z= 0.262 Angle : 0.696 10.193 10263 Z= 0.356 Chirality : 0.046 0.193 1204 Planarity : 0.005 0.050 1111 Dihedral : 17.394 82.873 1580 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.71 % Allowed : 33.53 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.30), residues: 751 helix: 0.55 (0.35), residues: 215 sheet: -0.92 (0.38), residues: 169 loop : -1.57 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 639 HIS 0.007 0.001 HIS A 946 PHE 0.031 0.002 PHE A 950 TYR 0.010 0.002 TYR A 888 ARG 0.012 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.666 Fit side-chains REVERT: A 288 GLU cc_start: 0.7213 (mp0) cc_final: 0.6802 (tp30) REVERT: A 290 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7719 (mmpt) REVERT: A 305 GLN cc_start: 0.7175 (tp40) cc_final: 0.6632 (tp40) REVERT: A 486 LYS cc_start: 0.5512 (OUTLIER) cc_final: 0.4093 (ttpt) REVERT: A 670 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7190 (mp) REVERT: A 682 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6563 (mp) REVERT: A 736 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6588 (mm110) REVERT: A 777 MET cc_start: 0.2640 (mmp) cc_final: 0.2181 (mmt) REVERT: A 801 ASN cc_start: 0.6054 (t0) cc_final: 0.5731 (t0) REVERT: A 852 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6293 (ttmm) REVERT: A 878 THR cc_start: 0.8322 (m) cc_final: 0.8034 (m) REVERT: A 942 CYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8342 (m) outliers start: 39 outliers final: 22 residues processed: 129 average time/residue: 0.8555 time to fit residues: 118.9242 Evaluate side-chains 124 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 942 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS A 736 GLN A 840 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.202769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.167532 restraints weight = 8477.385| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.08 r_work: 0.4096 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7400 Z= 0.303 Angle : 0.747 13.139 10263 Z= 0.378 Chirality : 0.047 0.317 1204 Planarity : 0.005 0.054 1111 Dihedral : 17.399 83.048 1580 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.12 % Allowed : 34.26 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.40 (0.30), residues: 751 helix: 0.35 (0.34), residues: 218 sheet: -1.02 (0.38), residues: 171 loop : -1.67 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 639 HIS 0.005 0.001 HIS A 353 PHE 0.028 0.002 PHE A 950 TYR 0.014 0.002 TYR A 458 ARG 0.012 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.738 Fit side-chains REVERT: A 288 GLU cc_start: 0.7213 (mp0) cc_final: 0.6797 (tp30) REVERT: A 305 GLN cc_start: 0.7314 (tp40) cc_final: 0.6720 (tp40) REVERT: A 486 LYS cc_start: 0.5284 (OUTLIER) cc_final: 0.3935 (ttpt) REVERT: A 613 MET cc_start: 0.5582 (mmp) cc_final: 0.5024 (mpt) REVERT: A 670 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7199 (mp) REVERT: A 682 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6590 (mp) REVERT: A 736 GLN cc_start: 0.6992 (tp-100) cc_final: 0.6775 (mm-40) REVERT: A 777 MET cc_start: 0.2775 (mmp) cc_final: 0.2294 (mmt) REVERT: A 801 ASN cc_start: 0.5850 (t0) cc_final: 0.5244 (t0) REVERT: A 852 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.6332 (ttmm) REVERT: A 878 THR cc_start: 0.8371 (m) cc_final: 0.8113 (m) outliers start: 35 outliers final: 23 residues processed: 127 average time/residue: 0.8278 time to fit residues: 113.8063 Evaluate side-chains 118 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.204386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.169222 restraints weight = 8543.586| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.08 r_work: 0.4082 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3970 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7400 Z= 0.261 Angle : 0.726 11.514 10263 Z= 0.366 Chirality : 0.047 0.322 1204 Planarity : 0.005 0.055 1111 Dihedral : 17.393 83.811 1580 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.39 % Allowed : 35.14 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.29 (0.30), residues: 751 helix: 0.45 (0.35), residues: 216 sheet: -1.00 (0.37), residues: 171 loop : -1.57 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 639 HIS 0.013 0.001 HIS A 946 PHE 0.028 0.002 PHE A 950 TYR 0.011 0.002 TYR A 770 ARG 0.013 0.001 ARG A 564 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.698 Fit side-chains REVERT: A 268 ASN cc_start: 0.6474 (m-40) cc_final: 0.5294 (p0) REVERT: A 288 GLU cc_start: 0.6938 (mp0) cc_final: 0.6526 (tp30) REVERT: A 305 GLN cc_start: 0.7216 (tp40) cc_final: 0.6628 (tp40) REVERT: A 613 MET cc_start: 0.5644 (mmp) cc_final: 0.5181 (mpt) REVERT: A 670 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7163 (mp) REVERT: A 682 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6556 (mp) REVERT: A 777 MET cc_start: 0.2628 (mmp) cc_final: 0.2193 (mmt) REVERT: A 801 ASN cc_start: 0.5845 (t0) cc_final: 0.5136 (t0) REVERT: A 852 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6275 (ttmm) REVERT: A 878 THR cc_start: 0.8354 (m) cc_final: 0.8074 (m) outliers start: 30 outliers final: 22 residues processed: 114 average time/residue: 0.8612 time to fit residues: 106.2066 Evaluate side-chains 117 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 75 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 13 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 HIS ** 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 = 0.4485 r_free = 0.4485 target = 0.207090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.171912 restraints weight = 8314.494| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.16 r_work: 0.4087 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3974 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7400 Z= 0.224 Angle : 0.687 9.213 10263 Z= 0.348 Chirality : 0.046 0.304 1204 Planarity : 0.005 0.056 1111 Dihedral : 17.362 84.971 1580 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.54 % Allowed : 34.70 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.15 (0.30), residues: 751 helix: 0.59 (0.35), residues: 215 sheet: -0.81 (0.38), residues: 165 loop : -1.56 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 639 HIS 0.010 0.001 HIS A 946 PHE 0.043 0.002 PHE A 950 TYR 0.012 0.001 TYR A 770 ARG 0.013 0.001 ARG A 564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5050.49 seconds wall clock time: 90 minutes 0.34 seconds (5400.34 seconds total)