Starting phenix.real_space_refine on Tue Apr 9 09:21:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/04_2024/8ucw_42142_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/04_2024/8ucw_42142.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/04_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_42142/04_2024/8ucw_42142_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/04_2024/8ucw_42142_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/04_2024/8ucw_42142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/04_2024/8ucw_42142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/04_2024/8ucw_42142_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/04_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 7.67, per 1000 atoms: 0.48 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: 13.73 Conformation dependent library (CDL) restraints added in 1.4 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: 8.72 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: 6.93 Time building geometry restraints manager: 13.92 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: 7021 35.74 - 71.47: 403 71.47 - 107.21: 16 107.21 - 142.95: 4 142.95 - 178.68: 1 Dihedral angle restraints: 7445 sinusoidal: 4470 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 7442 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.230 Extract box with map and model: 6.520 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 60.890 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.760 ------------------------------------------------------------------------------- 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 : 20.733 178.684 3401 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 : 1.205 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: 0.7483 time to fit residues: 62.5259 Evaluate side-chains 40 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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: 6.9990 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: 4.9990 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: 0.7821 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8562 Z= 0.244 Angle : 0.557 8.150 11876 Z= 0.297 Chirality : 0.042 0.227 1341 Planarity : 0.003 0.030 1294 Dihedral : 20.248 175.725 1660 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.03 % Allowed : 17.40 % Favored : 81.57 % 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: 1.68 (0.29), residues: 862 helix: 2.19 (0.28), residues: 357 sheet: 0.78 (0.43), residues: 140 loop : 0.25 (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 0.012 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 48 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 1.211 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: 8 outliers final: 3 residues processed: 44 average time/residue: 0.9516 time to fit residues: 51.3443 Evaluate side-chains 40 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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=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: 4.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 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: 0.7919 moved from start: 0.1997 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= 0.382 Angle : 0.618 7.636 11876 Z= 0.331 Chirality : 0.043 0.179 1341 Planarity : 0.004 0.057 1294 Dihedral : 20.067 174.697 1660 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.55 % Allowed : 18.04 % Favored : 80.41 % 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: 1.01 (0.29), residues: 862 helix: 1.56 (0.27), residues: 362 sheet: 0.28 (0.41), residues: 141 loop : 0.02 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 366 HIS 0.006 0.001 HIS A 582 PHE 0.014 0.002 PHE A 642 TYR 0.019 0.001 TYR A 871 ARG 0.020 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 48 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 1.211 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: A 410 MET cc_start: 0.8716 (tpp) cc_final: 0.8465 (tpp) outliers start: 12 outliers final: 7 residues processed: 47 average time/residue: 0.7109 time to fit residues: 42.8428 Evaluate side-chains 41 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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: 5.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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: 0.7896 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8562 Z= 0.224 Angle : 0.534 7.950 11876 Z= 0.288 Chirality : 0.042 0.140 1341 Planarity : 0.003 0.034 1294 Dihedral : 19.914 173.380 1660 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.29 % Allowed : 18.69 % Favored : 80.03 % 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: 1.84 (0.27), residues: 361 sheet: 0.34 (0.41), residues: 139 loop : 0.14 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A1150 PHE 0.009 0.001 PHE A 854 TYR 0.012 0.001 TYR A 871 ARG 0.002 0.000 ARG A1187 *********************** 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 45 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 1.361 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: A 410 MET cc_start: 0.8760 (tpp) cc_final: 0.8318 (tpp) outliers start: 10 outliers final: 6 residues processed: 43 average time/residue: 0.7758 time to fit residues: 42.1339 Evaluate side-chains 42 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 699 GLU 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: 1.9990 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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: 0.7917 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8562 Z= 0.239 Angle : 0.533 7.060 11876 Z= 0.286 Chirality : 0.042 0.137 1341 Planarity : 0.003 0.034 1294 Dihedral : 19.716 169.525 1660 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.45 % Allowed : 17.53 % Favored : 80.03 % 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: 1.34 (0.29), residues: 862 helix: 1.94 (0.27), residues: 367 sheet: 0.33 (0.42), residues: 138 loop : 0.10 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.009 0.001 HIS A 412 PHE 0.008 0.001 PHE A 362 TYR 0.014 0.001 TYR A 871 ARG 0.005 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 55 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 36 time to evaluate : 1.113 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: A 410 MET cc_start: 0.8665 (tpp) cc_final: 0.8347 (tpp) REVERT: A 647 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9174 (mm) outliers start: 19 outliers final: 11 residues processed: 51 average time/residue: 0.6681 time to fit residues: 43.2830 Evaluate side-chains 46 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 485 GLU 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 647 LEU 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 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: 0.1980 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.0670 chunk 88 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 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: 1.6122 ------------------------------------------------------------------------------- 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: 0.7909 moved from start: 0.2499 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= 0.187 Angle : 0.502 6.994 11876 Z= 0.274 Chirality : 0.041 0.136 1341 Planarity : 0.003 0.035 1294 Dihedral : 19.645 175.695 1660 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.80 % Allowed : 17.78 % Favored : 80.41 % 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: 1.45 (0.29), residues: 862 helix: 2.08 (0.27), residues: 368 sheet: 0.28 (0.42), residues: 139 loop : 0.16 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A 412 PHE 0.007 0.001 PHE A 854 TYR 0.010 0.001 TYR A 871 ARG 0.003 0.000 ARG A 342 *********************** 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 49 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 35 time to evaluate : 1.164 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: A 410 MET cc_start: 0.8674 (tpp) cc_final: 0.8257 (tpp) REVERT: A 647 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9152 (mm) outliers start: 14 outliers final: 13 residues processed: 45 average time/residue: 0.7609 time to fit residues: 43.0442 Evaluate side-chains 47 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 33 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 485 GLU 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 647 LEU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1012 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.6980 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: 2.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8562 Z= 0.260 Angle : 0.532 6.507 11876 Z= 0.290 Chirality : 0.042 0.136 1341 Planarity : 0.003 0.035 1294 Dihedral : 19.648 178.819 1660 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.58 % Allowed : 17.27 % 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: 1.27 (0.29), residues: 862 helix: 2.00 (0.27), residues: 367 sheet: 0.24 (0.42), residues: 138 loop : -0.05 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1156 HIS 0.005 0.001 HIS A 794 PHE 0.008 0.001 PHE A 854 TYR 0.015 0.001 TYR A 871 ARG 0.003 0.000 ARG A1163 *********************** 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 53 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 33 time to evaluate : 1.262 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: A 410 MET cc_start: 0.8664 (tpp) cc_final: 0.8262 (tpp) outliers start: 20 outliers final: 16 residues processed: 48 average time/residue: 0.5826 time to fit residues: 37.8288 Evaluate side-chains 48 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 32 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 544 MET 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 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: 4.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.0030 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.5348 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8562 Z= 0.140 Angle : 0.511 10.546 11876 Z= 0.272 Chirality : 0.041 0.136 1341 Planarity : 0.003 0.036 1294 Dihedral : 19.525 176.987 1660 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.42 % Allowed : 18.56 % Favored : 80.03 % 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: 1.61 (0.30), residues: 862 helix: 2.30 (0.28), residues: 361 sheet: 0.22 (0.41), residues: 148 loop : 0.23 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.006 0.001 PHE A 854 TYR 0.008 0.001 TYR A 953 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 42 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 1.293 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: A 410 MET cc_start: 0.8580 (tpp) cc_final: 0.8113 (tpp) outliers start: 11 outliers final: 10 residues processed: 40 average time/residue: 0.6500 time to fit residues: 33.8821 Evaluate side-chains 40 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 531 ASP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 647 LEU 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 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: 0.5980 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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: 0.7935 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 8562 Z= 0.238 Angle : 0.526 7.257 11876 Z= 0.285 Chirality : 0.041 0.136 1341 Planarity : 0.003 0.036 1294 Dihedral : 19.513 179.620 1660 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.80 % Allowed : 18.04 % 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: 1.48 (0.29), residues: 862 helix: 2.22 (0.28), residues: 361 sheet: 0.30 (0.42), residues: 140 loop : 0.06 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1156 HIS 0.005 0.001 HIS A 582 PHE 0.007 0.001 PHE A 854 TYR 0.013 0.001 TYR A 871 ARG 0.002 0.000 ARG A 522 *********************** 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 46 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 32 time to evaluate : 1.217 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: A 410 MET cc_start: 0.8628 (tpp) cc_final: 0.8181 (tpp) outliers start: 14 outliers final: 12 residues processed: 42 average time/residue: 0.6758 time to fit residues: 36.9843 Evaluate side-chains 44 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 859 ASP Chi-restraints excluded: chain A residue 953 TYR 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: 3.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.7910 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8562 Z= 0.162 Angle : 0.503 8.818 11876 Z= 0.271 Chirality : 0.041 0.136 1341 Planarity : 0.003 0.037 1294 Dihedral : 19.438 179.213 1660 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.03 % Allowed : 18.56 % Favored : 80.41 % 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: 1.66 (0.30), residues: 862 helix: 2.36 (0.28), residues: 361 sheet: 0.38 (0.42), residues: 140 loop : 0.17 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.002 0.001 HIS A1152 PHE 0.006 0.001 PHE A 854 TYR 0.008 0.001 TYR A 871 ARG 0.002 0.000 ARG A1163 ********************** 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 40 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 1.330 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: A 410 MET cc_start: 0.8599 (tpp) cc_final: 0.8122 (tpp) REVERT: A 598 TYR cc_start: 0.8108 (p90) cc_final: 0.7858 (p90) outliers start: 8 outliers final: 8 residues processed: 37 average time/residue: 0.7135 time to fit residues: 33.8533 Evaluate side-chains 40 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 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 1061 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.037422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.030062 restraints weight = 216803.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.031109 restraints weight = 98060.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.031733 restraints weight = 59985.152| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8562 Z= 0.139 Angle : 0.490 7.486 11876 Z= 0.265 Chirality : 0.041 0.135 1341 Planarity : 0.003 0.037 1294 Dihedral : 19.277 179.729 1660 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.42 % Allowed : 18.17 % Favored : 80.41 % 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: 1.88 (0.30), residues: 862 helix: 2.58 (0.28), residues: 361 sheet: 0.51 (0.42), residues: 140 loop : 0.24 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.004 0.001 PHE A 568 TYR 0.010 0.001 TYR A 938 ARG 0.002 0.000 ARG A 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3659.37 seconds wall clock time: 66 minutes 9.81 seconds (3969.81 seconds total)