Starting phenix.real_space_refine on Sun Dec 10 23:45:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/12_2023/8ucw_42142_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/12_2023/8ucw_42142.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/12_2023/8ucw_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_42142/12_2023/8ucw_42142_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/12_2023/8ucw_42142_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/12_2023/8ucw_42142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/12_2023/8ucw_42142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/12_2023/8ucw_42142_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucw_42142/12_2023/8ucw_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-1.21rc1-5172/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: 8.39, per 1000 atoms: 0.53 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: 14.43 Conformation dependent library (CDL) restraints added in 1.7 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: 11.25 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: 7.15 Time building geometry restraints manager: 14.55 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: 6920 35.74 - 71.47: 359 71.47 - 107.21: 16 107.21 - 142.95: 4 142.95 - 178.68: 1 Dihedral angle restraints: 7300 sinusoidal: 4325 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 7297 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: 0.010 Normalize map: mean=0, sd=1: 1.600 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: 6.420 Check model and map are aligned: 0.280 Set scattering table: 0.210 Process input model: 66.300 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.110 ------------------------------------------------------------------------------- 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 : 1.283 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: 0.7526 time to fit residues: 63.0389 Evaluate side-chains 40 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5855 ------------------------------------------------------------------------------- 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: 0.8980 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 HIS A 770 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8562 Z= 0.182 Angle : 0.534 8.245 11876 Z= 0.284 Chirality : 0.041 0.203 1341 Planarity : 0.003 0.032 1294 Dihedral : 20.127 175.779 1652 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.90 % Allowed : 17.14 % Favored : 81.96 % 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: 1.80 (0.30), residues: 862 helix: 2.26 (0.28), residues: 356 sheet: 0.99 (0.44), residues: 138 loop : 0.28 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1156 HIS 0.002 0.001 HIS A 582 PHE 0.008 0.001 PHE A 362 TYR 0.010 0.001 TYR A 706 ARG 0.003 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 47 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 1.411 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 outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 0.9901 time to fit residues: 52.9497 Evaluate side-chains 41 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 1.330 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3731 time to fit residues: 3.1606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 68 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8562 Z= 0.380 Angle : 0.612 7.659 11876 Z= 0.328 Chirality : 0.043 0.180 1341 Planarity : 0.003 0.031 1294 Dihedral : 19.910 175.026 1652 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.42 % Allowed : 17.65 % Favored : 80.93 % 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: 1.16 (0.29), residues: 862 helix: 1.67 (0.27), residues: 362 sheet: 0.43 (0.42), residues: 140 loop : 0.09 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.006 0.001 HIS A 582 PHE 0.011 0.002 PHE A 362 TYR 0.019 0.001 TYR A 871 ARG 0.004 0.000 ARG A1187 *********************** 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 49 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 1.327 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 outliers start: 11 outliers final: 5 residues processed: 48 average time/residue: 0.7827 time to fit residues: 47.6632 Evaluate side-chains 42 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1981 time to fit residues: 3.3408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8562 Z= 0.157 Angle : 0.517 8.192 11876 Z= 0.277 Chirality : 0.041 0.148 1341 Planarity : 0.003 0.066 1294 Dihedral : 19.736 176.062 1652 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.52 % Allowed : 17.91 % 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: 1.57 (0.29), residues: 862 helix: 2.05 (0.28), residues: 362 sheet: 0.55 (0.42), residues: 138 loop : 0.31 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A 794 PHE 0.008 0.001 PHE A 642 TYR 0.008 0.001 TYR A 871 ARG 0.002 0.000 ARG A 778 *********************** 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 41 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.7838 time to fit residues: 39.2148 Evaluate side-chains 40 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1772 time to fit residues: 2.4403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 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: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8562 Z= 0.286 Angle : 0.554 7.336 11876 Z= 0.299 Chirality : 0.042 0.136 1341 Planarity : 0.003 0.032 1294 Dihedral : 19.612 159.455 1652 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.77 % Allowed : 17.91 % Favored : 81.31 % 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: 1.22 (0.29), residues: 862 helix: 1.83 (0.27), residues: 362 sheet: 0.36 (0.42), residues: 138 loop : 0.03 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.005 0.001 HIS A 582 PHE 0.009 0.001 PHE A 854 TYR 0.015 0.001 TYR A 871 ARG 0.004 0.000 ARG A 491 *********************** 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 41 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 1.372 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 outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 0.7908 time to fit residues: 40.4621 Evaluate side-chains 38 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4086 time to fit residues: 3.2642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2298 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= 0.177 Angle : 0.505 7.261 11876 Z= 0.273 Chirality : 0.041 0.135 1341 Planarity : 0.003 0.038 1294 Dihedral : 19.545 170.765 1652 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.26 % Allowed : 18.69 % Favored : 81.06 % 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: 1.47 (0.29), residues: 862 helix: 2.09 (0.28), residues: 367 sheet: 0.34 (0.42), residues: 140 loop : 0.14 (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 582 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 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 38 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 1.324 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 outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.8153 time to fit residues: 38.2668 Evaluate side-chains 35 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1934 time to fit residues: 1.9503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 0.0270 overall best weight: 1.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8562 Z= 0.215 Angle : 0.512 6.645 11876 Z= 0.279 Chirality : 0.041 0.136 1341 Planarity : 0.003 0.034 1294 Dihedral : 19.461 178.272 1652 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.52 % Allowed : 18.17 % Favored : 81.31 % 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: 1.42 (0.29), residues: 862 helix: 2.10 (0.27), residues: 367 sheet: 0.34 (0.42), residues: 138 loop : 0.04 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.004 0.001 HIS A 582 PHE 0.008 0.001 PHE A 362 TYR 0.013 0.001 TYR A 871 ARG 0.002 0.000 ARG A1187 *********************** 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 40 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 1.215 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: 4 outliers final: 3 residues processed: 40 average time/residue: 0.7742 time to fit residues: 39.3325 Evaluate side-chains 39 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2270 time to fit residues: 2.6972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.0040 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 0.0570 chunk 84 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8562 Z= 0.130 Angle : 0.490 8.585 11876 Z= 0.263 Chirality : 0.040 0.135 1341 Planarity : 0.003 0.036 1294 Dihedral : 19.318 178.209 1652 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.26 % Allowed : 17.78 % Favored : 81.96 % 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: 1.82 (0.30), residues: 862 helix: 2.39 (0.28), residues: 367 sheet: 0.57 (0.43), residues: 139 loop : 0.31 (0.35), residues: 356 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 583 TYR 0.013 0.001 TYR A 953 ARG 0.002 0.000 ARG A1020 *********************** 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 37 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 1.306 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 outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.8186 time to fit residues: 37.2862 Evaluate side-chains 33 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1839 time to fit residues: 1.9011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8562 Z= 0.181 Angle : 0.509 8.714 11876 Z= 0.273 Chirality : 0.041 0.136 1341 Planarity : 0.003 0.035 1294 Dihedral : 19.281 179.823 1652 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.13 % Allowed : 17.78 % Favored : 82.09 % 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: 1.79 (0.30), residues: 862 helix: 2.38 (0.28), residues: 367 sheet: 0.57 (0.43), residues: 139 loop : 0.25 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.006 0.001 HIS A 412 PHE 0.006 0.001 PHE A 362 TYR 0.010 0.001 TYR A 953 ARG 0.002 0.000 ARG A1163 *********************** 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 34 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 1.248 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 outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.6914 time to fit residues: 29.9688 Evaluate side-chains 34 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1911 time to fit residues: 1.8618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 90 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2691 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= 0.162 Angle : 0.511 10.111 11876 Z= 0.272 Chirality : 0.041 0.133 1341 Planarity : 0.003 0.035 1294 Dihedral : 19.236 178.972 1652 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.26 % Allowed : 17.78 % Favored : 81.96 % 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: 1.82 (0.30), residues: 862 helix: 2.40 (0.28), residues: 367 sheet: 0.60 (0.43), residues: 139 loop : 0.27 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.002 0.001 HIS A 412 PHE 0.005 0.001 PHE A 854 TYR 0.010 0.001 TYR A 953 ARG 0.002 0.000 ARG A1187 ********************** 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 35 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 1.407 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 outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.6852 time to fit residues: 29.8379 Evaluate side-chains 35 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2201 time to fit residues: 2.4621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 0.0670 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.037523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.030050 restraints weight = 214383.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.031096 restraints weight = 97602.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.031735 restraints weight = 59548.146| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8562 Z= 0.159 Angle : 0.500 6.634 11876 Z= 0.269 Chirality : 0.041 0.140 1341 Planarity : 0.003 0.035 1294 Dihedral : 19.157 177.143 1652 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 17.78 % Favored : 82.22 % 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: 1.85 (0.30), residues: 862 helix: 2.46 (0.28), residues: 368 sheet: 0.61 (0.43), residues: 139 loop : 0.23 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.003 0.001 HIS A 412 PHE 0.005 0.001 PHE A 362 TYR 0.009 0.001 TYR A 871 ARG 0.002 0.000 ARG A1187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3724.11 seconds wall clock time: 66 minutes 45.48 seconds (4005.48 seconds total)