Starting phenix.real_space_refine on Sat Jan 20 17:51:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/01_2024/8ucw_42142_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/01_2024/8ucw_42142.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/01_2024/8ucw_42142_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/01_2024/8ucw_42142_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/01_2024/8ucw_42142_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/01_2024/8ucw_42142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/01_2024/8ucw_42142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/01_2024/8ucw_42142_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/01_2024/8ucw_42142_trim_updated.pdb" } resolution = 3.64 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= 0.002 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: 7 Type Number sf(0) Gaussians P 67 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 5063 2.51 5 N 1411 2.21 5 O 1688 1.98 5 H 7703 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15967 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 13976 Classifications: {'peptide': 868} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 822} Chain breaks: 2 Chain: "C" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1042 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 916 Unusual residues: {'DOC': 1, 'GTP': 1} Classifications: {'DNA': 19, 'RNA': 8, 'undetermined': 2} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 26, None: 2} Not linked: pdbres="GTP D 1 " pdbres=" G D 2 " Not linked: pdbres=" DG D 28 " pdbres="DOC D 29 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'DGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" 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: 8.57, per 1000 atoms: 0.54 Number of scatterers: 15967 At special positions: 0 Unit cell: (115.893, 94.0266, 153.067, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 33 16.00 P 67 15.00 Mg 2 11.99 O 1688 8.00 N 1411 7.00 C 5063 6.00 H 7703 1.00 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 6 sheets defined 38.5% alpha, 15.2% beta 27 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 8.00 Creating SS restraints... Processing helix chain 'A' and resid 410 through 419 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 643 through 654 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 735 through 759 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 785 through 799 removed outlier: 3.539A pdb=" N ASN A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'A' and resid 906 through 926 Processing helix chain 'A' and resid 932 through 957 removed outlier: 4.080A pdb=" N LEU A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 990 Processing helix chain 'A' and resid 1011 through 1028 removed outlier: 4.262A pdb=" N SER A1028 " --> pdb=" O GLU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1076 No H-bonds generated for 'chain 'A' and resid 1074 through 1076' Processing helix chain 'A' and resid 1082 through 1096 Processing helix chain 'A' and resid 1101 through 1121 Processing helix chain 'A' and resid 1126 through 1129 Processing helix chain 'A' and resid 1149 through 1159 Processing helix chain 'A' and resid 1184 through 1186 No H-bonds generated for 'chain 'A' and resid 1184 through 1186' Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1204 through 1210 Processing helix chain 'A' and resid 1213 through 1219 Processing helix chain 'A' and resid 1228 through 1234 Processing sheet with id= A, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.933A pdb=" N SER A 497 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ARG A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TRP A 366 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA A 348 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 372 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 516 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N SER A 379 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA A 518 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS A 381 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 520 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 385 through 387 Processing sheet with id= C, first strand: chain 'A' and resid 689 through 692 removed outlier: 6.202A pdb=" N VAL A 547 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE A 557 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN A 549 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASN A 555 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 558 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 849 through 851 removed outlier: 7.143A pdb=" N LYS A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1001 through 1005 removed outlier: 3.678A pdb=" N GLY A1038 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP A 859 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE A1036 " --> pdb=" O ASP A 859 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1131 through 1133 293 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 5.87 Time building geometry restraints manager: 14.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7687 1.03 - 1.23: 46 1.23 - 1.42: 3557 1.42 - 1.62: 4925 1.62 - 1.81: 50 Bond restraints: 16265 Sorted by residual: bond pdb=" C2' DGT A1501 " pdb=" C3' DGT A1501 " ideal model delta sigma weight residual 1.284 1.543 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C4' DOC D 29 " pdb=" C3' DOC D 29 " ideal model delta sigma weight residual 1.334 1.547 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C4' DGT A1501 " pdb=" O4' DGT A1501 " ideal model delta sigma weight residual 1.272 1.450 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" O4' DOC D 29 " pdb=" C1' DOC D 29 " ideal model delta sigma weight residual 1.268 1.440 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" C2 DOC D 29 " pdb=" N3 DOC D 29 " ideal model delta sigma weight residual 1.492 1.330 0.162 2.00e-02 2.50e+03 6.59e+01 ... (remaining 16260 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.08: 500 106.08 - 113.19: 19011 113.19 - 120.30: 5449 120.30 - 127.41: 4352 127.41 - 134.52: 183 Bond angle restraints: 29495 Sorted by residual: angle pdb=" PA GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PB GTP D 1 " ideal model delta sigma weight residual 120.50 132.98 -12.48 3.00e+00 1.11e-01 1.73e+01 angle pdb=" PB GTP D 1 " pdb=" O3B GTP D 1 " pdb=" PG GTP D 1 " ideal model delta sigma weight residual 120.50 132.58 -12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C2' GTP D 1 " pdb=" C3' GTP D 1 " pdb=" C4' GTP D 1 " ideal model delta sigma weight residual 111.00 98.98 12.02 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C1' GTP D 1 " pdb=" C2' GTP D 1 " pdb=" C3' GTP D 1 " ideal model delta sigma weight residual 111.00 100.28 10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" OP1 DOC D 29 " pdb=" P DOC D 29 " pdb=" OP2 DOC D 29 " ideal model delta sigma weight residual 109.57 119.95 -10.38 3.00e+00 1.11e-01 1.20e+01 ... (remaining 29490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 6975 35.74 - 71.47: 359 71.47 - 107.21: 16 107.21 - 142.95: 4 142.95 - 178.68: 1 Dihedral angle restraints: 7355 sinusoidal: 4380 harmonic: 2975 Sorted by residual: dihedral pdb=" C4' GTP D 1 " pdb=" C5' GTP D 1 " pdb=" O5' GTP D 1 " pdb=" PA GTP D 1 " ideal model delta sinusoidal sigma weight residual 260.87 82.19 178.68 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PB GTP D 1 " pdb=" PA GTP D 1 " ideal model delta sinusoidal sigma weight residual -68.92 69.07 -137.99 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" O5' GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PA GTP D 1 " pdb=" PB GTP D 1 " ideal model delta sinusoidal sigma weight residual 274.12 146.64 127.48 1 2.00e+01 2.50e-03 3.86e+01 ... (remaining 7352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1178 0.069 - 0.137: 155 0.137 - 0.206: 4 0.206 - 0.275: 2 0.275 - 0.343: 2 Chirality restraints: 1341 Sorted by residual: chirality pdb=" C3' DGT A1501 " pdb=" C2' DGT A1501 " pdb=" C4' DGT A1501 " pdb=" O3' DGT A1501 " both_signs ideal model delta sigma weight residual False -2.42 -2.77 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C2' GTP D 1 " pdb=" C1' GTP D 1 " pdb=" C3' GTP D 1 " pdb=" O2' GTP D 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.78 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C3' GTP D 1 " pdb=" C2' GTP D 1 " pdb=" C4' GTP D 1 " pdb=" O3' GTP D 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1338 not shown) Planarity restraints: 2157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 864 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 865 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 865 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 865 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 907 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 908 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 908 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 908 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 28 " -0.015 2.00e-02 2.50e+03 6.79e-03 1.38e+00 pdb=" N1 DT C 28 " 0.018 2.00e-02 2.50e+03 pdb=" C2 DT C 28 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT C 28 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DT C 28 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT C 28 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT C 28 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DT C 28 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT C 28 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT C 28 " 0.001 2.00e-02 2.50e+03 pdb=" H3 DT C 28 " -0.001 2.00e-02 2.50e+03 pdb=" H6 DT C 28 " 0.001 2.00e-02 2.50e+03 ... (remaining 2154 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 781 2.19 - 2.79: 30853 2.79 - 3.40: 43004 3.40 - 4.00: 58315 4.00 - 4.60: 87573 Nonbonded interactions: 220526 Sorted by model distance: nonbonded pdb=" OD1 ASP A 351 " pdb=" H SER A 354 " model vdw 1.590 1.850 nonbonded pdb=" H GLN A1177 " pdb=" O SER A1201 " model vdw 1.626 1.850 nonbonded pdb=" OE1 GLU A 350 " pdb=" H LEU A 484 " model vdw 1.674 1.850 nonbonded pdb=" OD1 ASP A1227 " pdb=" H LEU A1230 " model vdw 1.684 1.850 nonbonded pdb=" O LYS A 847 " pdb=" HH TYR A 851 " model vdw 1.688 1.850 ... (remaining 220521 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.220 Extract box with map and model: 7.040 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 60.930 Find NCS groups from input model: 0.260 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 0.259 8562 Z= 0.414 Angle : 0.568 12.477 11876 Z= 0.282 Chirality : 0.045 0.343 1341 Planarity : 0.003 0.032 1294 Dihedral : 20.680 178.684 3393 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 17.01 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.69 (0.30), residues: 862 helix: 2.12 (0.29), residues: 352 sheet: 0.70 (0.44), residues: 147 loop : 0.41 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 659 HIS 0.002 0.001 HIS A 707 PHE 0.006 0.001 PHE A 583 TYR 0.008 0.001 TYR A 964 ARG 0.002 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.7572 time to fit residues: 63.3993 Evaluate side-chains 40 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8562 Z= 0.246 Angle : 0.560 8.038 11876 Z= 0.298 Chirality : 0.042 0.218 1341 Planarity : 0.003 0.030 1294 Dihedral : 20.138 175.491 1652 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.16 % Allowed : 17.14 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.67 (0.29), residues: 862 helix: 2.18 (0.28), residues: 357 sheet: 0.78 (0.43), residues: 140 loop : 0.24 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 498 HIS 0.003 0.001 HIS A 582 PHE 0.008 0.001 PHE A 362 TYR 0.013 0.001 TYR A 706 ARG 0.004 0.000 ARG A 778 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 0.8824 time to fit residues: 48.4675 Evaluate side-chains 41 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 984 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.006 0.044 8562 Z= 0.393 Angle : 0.626 7.638 11876 Z= 0.336 Chirality : 0.044 0.169 1341 Planarity : 0.004 0.068 1294 Dihedral : 19.935 174.825 1652 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.55 % Allowed : 18.30 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.88 (0.28), residues: 862 helix: 1.46 (0.27), residues: 362 sheet: 0.26 (0.41), residues: 142 loop : -0.08 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 366 HIS 0.006 0.001 HIS A 582 PHE 0.019 0.002 PHE A 642 TYR 0.020 0.002 TYR A 871 ARG 0.034 0.001 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 35 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 46 average time/residue: 0.6978 time to fit residues: 41.3080 Evaluate side-chains 40 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 1012 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8562 Z= 0.196 Angle : 0.531 8.380 11876 Z= 0.284 Chirality : 0.042 0.137 1341 Planarity : 0.003 0.034 1294 Dihedral : 19.766 172.057 1652 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.16 % Allowed : 19.20 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.28 (0.29), residues: 862 helix: 1.81 (0.27), residues: 367 sheet: 0.36 (0.41), residues: 139 loop : 0.14 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A1150 PHE 0.008 0.001 PHE A 854 TYR 0.010 0.001 TYR A 871 ARG 0.002 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 42 average time/residue: 0.7660 time to fit residues: 40.3058 Evaluate side-chains 39 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 742 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8562 Z= 0.294 Angle : 0.565 7.065 11876 Z= 0.303 Chirality : 0.042 0.137 1341 Planarity : 0.003 0.033 1294 Dihedral : 19.647 163.969 1652 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.06 % Allowed : 18.30 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.08 (0.29), residues: 862 helix: 1.73 (0.27), residues: 368 sheet: 0.28 (0.42), residues: 138 loop : -0.08 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.007 0.001 HIS A 412 PHE 0.010 0.001 PHE A 854 TYR 0.016 0.001 TYR A 871 ARG 0.004 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 35 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 47 average time/residue: 0.6745 time to fit residues: 40.5922 Evaluate side-chains 44 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1138 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8562 Z= 0.279 Angle : 0.547 8.299 11876 Z= 0.297 Chirality : 0.042 0.137 1341 Planarity : 0.003 0.034 1294 Dihedral : 19.668 176.759 1652 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.58 % Allowed : 17.53 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.95 (0.29), residues: 862 helix: 1.70 (0.27), residues: 368 sheet: 0.14 (0.41), residues: 138 loop : -0.22 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.005 0.001 HIS A 582 PHE 0.010 0.001 PHE A 854 TYR 0.015 0.001 TYR A 871 ARG 0.003 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 34 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 50 average time/residue: 0.6693 time to fit residues: 43.0588 Evaluate side-chains 46 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 32 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1138 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8562 Z= 0.289 Angle : 0.560 8.812 11876 Z= 0.303 Chirality : 0.042 0.138 1341 Planarity : 0.003 0.035 1294 Dihedral : 19.687 178.987 1652 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.45 % Allowed : 18.43 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.84 (0.29), residues: 862 helix: 1.71 (0.27), residues: 361 sheet: 0.04 (0.41), residues: 138 loop : -0.35 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.005 0.001 HIS A 582 PHE 0.010 0.001 PHE A 854 TYR 0.015 0.001 TYR A 871 ARG 0.003 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 32 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 17 residues processed: 47 average time/residue: 0.5741 time to fit residues: 35.8090 Evaluate side-chains 47 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 30 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1138 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 0.0070 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8562 Z= 0.161 Angle : 0.514 8.748 11876 Z= 0.277 Chirality : 0.041 0.137 1341 Planarity : 0.003 0.036 1294 Dihedral : 19.550 178.155 1652 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.68 % Allowed : 19.33 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.24 (0.29), residues: 862 helix: 2.10 (0.28), residues: 361 sheet: 0.10 (0.42), residues: 138 loop : -0.14 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.007 0.001 PHE A 854 TYR 0.009 0.001 TYR A 871 ARG 0.002 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 42 average time/residue: 0.6390 time to fit residues: 35.3388 Evaluate side-chains 41 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1061 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8562 Z= 0.172 Angle : 0.510 9.133 11876 Z= 0.274 Chirality : 0.041 0.136 1341 Planarity : 0.003 0.036 1294 Dihedral : 19.422 179.089 1652 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.55 % Allowed : 19.59 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.43 (0.29), residues: 862 helix: 2.26 (0.28), residues: 361 sheet: 0.20 (0.42), residues: 138 loop : -0.04 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.011 0.001 HIS A 794 PHE 0.005 0.001 PHE A 854 TYR 0.009 0.001 TYR A 871 ARG 0.002 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 41 average time/residue: 0.7034 time to fit residues: 36.5574 Evaluate side-chains 43 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1061 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 8562 Z= 0.294 Angle : 0.569 9.554 11876 Z= 0.308 Chirality : 0.042 0.141 1341 Planarity : 0.003 0.034 1294 Dihedral : 19.493 176.763 1652 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.68 % Allowed : 19.33 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.99 (0.29), residues: 862 helix: 1.90 (0.28), residues: 362 sheet: 0.00 (0.41), residues: 138 loop : -0.30 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 366 HIS 0.007 0.001 HIS A 582 PHE 0.011 0.001 PHE A 854 TYR 0.017 0.001 TYR A 871 ARG 0.004 0.000 ARG A 522 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 13 residues processed: 41 average time/residue: 0.6592 time to fit residues: 35.1660 Evaluate side-chains 45 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1061 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** 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 = 0.3461 r_free = 0.3461 target = 0.036936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.029697 restraints weight = 217185.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.030730 restraints weight = 97559.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.031313 restraints weight = 59405.018| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8562 Z= 0.157 Angle : 0.512 9.757 11876 Z= 0.274 Chirality : 0.041 0.135 1341 Planarity : 0.003 0.037 1294 Dihedral : 19.392 177.937 1652 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.68 % Allowed : 19.20 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.35 (0.29), residues: 862 helix: 2.22 (0.28), residues: 361 sheet: 0.09 (0.42), residues: 138 loop : -0.08 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.006 0.001 PHE A 854 TYR 0.009 0.001 TYR A 425 ARG 0.002 0.000 ARG A1020 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3534.42 seconds wall clock time: 64 minutes 4.71 seconds (3844.71 seconds total)