Starting phenix.real_space_refine on Thu Dec 7 23:30:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1j_34428/12_2023/8h1j_34428.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1j_34428/12_2023/8h1j_34428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1j_34428/12_2023/8h1j_34428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1j_34428/12_2023/8h1j_34428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1j_34428/12_2023/8h1j_34428.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1j_34428/12_2023/8h1j_34428.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.134 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 134 5.49 5 S 6 5.16 5 C 3147 2.51 5 N 1063 2.21 5 O 1422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5773 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2930 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "B" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2185 Classifications: {'RNA': 102} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 52, 'rna3p_pyr': 43} Link IDs: {'rna2p': 7, 'rna3p': 94} Chain breaks: 2 Chain: "D" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2567 SG CYS A 331 56.562 13.710 50.711 1.00192.35 S ATOM 2591 SG CYS A 334 56.015 10.341 49.439 1.00215.36 S ATOM 2728 SG CYS A 351 54.453 10.050 52.311 1.00222.37 S ATOM 2749 SG CYS A 354 57.190 11.215 52.766 1.00225.00 S Time building chain proxies: 3.86, per 1000 atoms: 0.67 Number of scatterers: 5773 At special positions: 0 Unit cell: (77.024, 102.256, 104.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 6 16.00 P 134 15.00 O 1422 8.00 N 1063 7.00 C 3147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 691.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 331 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 351 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 354 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 334 " Number of angles added : 6 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 674 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 4 sheets defined 48.6% alpha, 20.4% beta 57 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 14 through 47 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.857A pdb=" N LEU A 71 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 removed outlier: 3.711A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 236 through 271 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 360 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.935A pdb=" N GLU A 116 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N LYS A 153 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU A 176 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 155 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLU A 174 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL A 157 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU A 172 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 159 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER A 170 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ARG A 161 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU A 168 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 163 " --> pdb=" O HIS A 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 10 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS A 143 " --> pdb=" O TYR A 12 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 128 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.761A pdb=" N PHE A 186 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU A 278 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU A 273 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER A 319 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 275 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL A 321 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A 277 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 351 removed outlier: 3.918A pdb=" N TRP A 349 " --> pdb=" O HIS A 358 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1031 1.33 - 1.45: 2200 1.45 - 1.57: 2666 1.57 - 1.69: 263 1.69 - 1.81: 7 Bond restraints: 6167 Sorted by residual: bond pdb=" C1' G B -45 " pdb=" N9 G B -45 " ideal model delta sigma weight residual 1.475 1.455 0.020 1.50e-02 4.44e+03 1.78e+00 bond pdb=" O5' C B-107 " pdb=" C5' C B-107 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.64e+00 bond pdb=" N9 G B -45 " pdb=" C4 G B -45 " ideal model delta sigma weight residual 1.375 1.400 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" CB TRP A 313 " pdb=" CG TRP A 313 " ideal model delta sigma weight residual 1.498 1.461 0.037 3.10e-02 1.04e+03 1.41e+00 bond pdb=" C5 DC D -8 " pdb=" C6 DC D -8 " ideal model delta sigma weight residual 1.337 1.360 -0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 6162 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.23: 782 106.23 - 113.17: 3497 113.17 - 120.10: 2197 120.10 - 127.04: 2136 127.04 - 133.98: 340 Bond angle restraints: 8952 Sorted by residual: angle pdb=" N VAL A 346 " pdb=" CA VAL A 346 " pdb=" C VAL A 346 " ideal model delta sigma weight residual 106.21 109.76 -3.55 1.07e+00 8.73e-01 1.10e+01 angle pdb=" O3' C B-107 " pdb=" C3' C B-107 " pdb=" C2' C B-107 " ideal model delta sigma weight residual 113.70 109.43 4.27 1.50e+00 4.44e-01 8.09e+00 angle pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 113.90 118.12 -4.22 1.80e+00 3.09e-01 5.49e+00 angle pdb=" C HIS A 34 " pdb=" N PHE A 35 " pdb=" CA PHE A 35 " ideal model delta sigma weight residual 121.14 117.32 3.82 1.75e+00 3.27e-01 4.76e+00 angle pdb=" CA VAL A 346 " pdb=" C VAL A 346 " pdb=" O VAL A 346 " ideal model delta sigma weight residual 122.63 120.76 1.87 8.70e-01 1.32e+00 4.64e+00 ... (remaining 8947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 2979 18.12 - 36.25: 335 36.25 - 54.37: 216 54.37 - 72.49: 117 72.49 - 90.62: 27 Dihedral angle restraints: 3674 sinusoidal: 2625 harmonic: 1049 Sorted by residual: dihedral pdb=" CA PHE A 35 " pdb=" C PHE A 35 " pdb=" N LEU A 36 " pdb=" CA LEU A 36 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 dihedral pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " pdb=" CG LEU A 222 " ideal model delta sinusoidal sigma weight residual -180.00 -120.80 -59.20 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS A 143 " pdb=" CB LYS A 143 " pdb=" CG LYS A 143 " pdb=" CD LYS A 143 " ideal model delta sinusoidal sigma weight residual -60.00 -118.40 58.40 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 3671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 805 0.033 - 0.067: 201 0.067 - 0.100: 47 0.100 - 0.134: 13 0.134 - 0.167: 4 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C1' A B -88 " pdb=" O4' A B -88 " pdb=" C2' A B -88 " pdb=" N9 A B -88 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA PHE A 35 " pdb=" N PHE A 35 " pdb=" C PHE A 35 " pdb=" CB PHE A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" C3' C B-107 " pdb=" C4' C B-107 " pdb=" O3' C B-107 " pdb=" C2' C B-107 " both_signs ideal model delta sigma weight residual False -2.48 -2.62 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1067 not shown) Planarity restraints: 648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C 21 " -0.029 2.00e-02 2.50e+03 1.26e-02 4.34e+00 pdb=" N9 DA C 21 " 0.005 2.00e-02 2.50e+03 pdb=" C8 DA C 21 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DA C 21 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DA C 21 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DA C 21 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA C 21 " -0.022 2.00e-02 2.50e+03 pdb=" N1 DA C 21 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA C 21 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA C 21 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA C 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -96 " -0.026 2.00e-02 2.50e+03 1.09e-02 3.58e+00 pdb=" N9 G B -96 " 0.025 2.00e-02 2.50e+03 pdb=" C8 G B -96 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B -96 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B -96 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B -96 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B -96 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B -96 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B -96 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B -96 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B -96 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G B -96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 106 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 107 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " 0.025 5.00e-02 4.00e+02 ... (remaining 645 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1045 2.77 - 3.30: 5147 3.30 - 3.83: 11172 3.83 - 4.37: 13054 4.37 - 4.90: 18820 Nonbonded interactions: 49238 Sorted by model distance: nonbonded pdb=" N2 G B-112 " pdb=" N6 A B -86 " model vdw 2.232 2.560 nonbonded pdb=" O2' G B-111 " pdb=" N4 C B -85 " model vdw 2.293 2.520 nonbonded pdb=" NH1 ARG A 270 " pdb=" OP1 A B -1 " model vdw 2.303 2.520 nonbonded pdb=" NH1 ARG A 110 " pdb=" OP1 C B 5 " model vdw 2.347 2.520 nonbonded pdb=" OG1 THR A 114 " pdb=" OP1 DA C 8 " model vdw 2.356 2.440 ... (remaining 49233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.140 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 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 : 0.005 0.044 6167 Z= 0.287 Angle : 0.533 4.266 8952 Z= 0.306 Chirality : 0.034 0.167 1070 Planarity : 0.004 0.044 648 Dihedral : 21.476 90.616 3000 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.19 % Allowed : 9.74 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.45), residues: 358 helix: 2.39 (0.37), residues: 173 sheet: 0.49 (0.60), residues: 81 loop : 0.79 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 349 HIS 0.005 0.001 HIS A 163 PHE 0.026 0.002 PHE A 35 TYR 0.024 0.002 TYR A 309 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.425 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 69 average time/residue: 0.2771 time to fit residues: 22.8728 Evaluate side-chains 33 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0625 time to fit residues: 1.2783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6167 Z= 0.188 Angle : 0.481 5.201 8952 Z= 0.268 Chirality : 0.033 0.160 1070 Planarity : 0.004 0.044 648 Dihedral : 22.130 91.818 2269 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.95 % Allowed : 15.26 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.45), residues: 358 helix: 2.50 (0.37), residues: 175 sheet: 0.61 (0.64), residues: 79 loop : 0.76 (0.64), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 349 HIS 0.004 0.001 HIS A 163 PHE 0.020 0.002 PHE A 35 TYR 0.019 0.001 TYR A 309 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.426 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 31 average time/residue: 0.1778 time to fit residues: 7.6353 Evaluate side-chains 23 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0707 time to fit residues: 0.7672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 0.3980 chunk 37 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6167 Z= 0.202 Angle : 0.472 4.661 8952 Z= 0.264 Chirality : 0.033 0.156 1070 Planarity : 0.004 0.044 648 Dihedral : 22.075 92.368 2269 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.60 % Allowed : 15.91 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.45), residues: 358 helix: 2.54 (0.37), residues: 175 sheet: 0.32 (0.65), residues: 73 loop : 0.79 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 349 HIS 0.003 0.001 HIS A 163 PHE 0.024 0.002 PHE A 35 TYR 0.017 0.001 TYR A 309 ARG 0.002 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.414 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 31 average time/residue: 0.1929 time to fit residues: 8.1525 Evaluate side-chains 30 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1289 time to fit residues: 1.4105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6167 Z= 0.261 Angle : 0.512 4.297 8952 Z= 0.283 Chirality : 0.035 0.189 1070 Planarity : 0.004 0.043 648 Dihedral : 22.121 94.137 2269 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.30 % Allowed : 15.91 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.95 (0.45), residues: 358 helix: 2.31 (0.38), residues: 175 sheet: 0.06 (0.64), residues: 75 loop : 0.67 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 349 HIS 0.004 0.001 HIS A 163 PHE 0.026 0.002 PHE A 35 TYR 0.024 0.002 TYR A 309 ARG 0.002 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.428 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 33 average time/residue: 0.2203 time to fit residues: 9.4889 Evaluate side-chains 24 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0535 time to fit residues: 0.5917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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: 0.6583 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6167 Z= 0.289 Angle : 0.535 6.567 8952 Z= 0.293 Chirality : 0.036 0.194 1070 Planarity : 0.004 0.045 648 Dihedral : 22.227 95.051 2269 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.27 % Allowed : 15.91 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.70 (0.45), residues: 358 helix: 2.16 (0.38), residues: 175 sheet: -0.19 (0.63), residues: 75 loop : 0.55 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 349 HIS 0.004 0.001 HIS A 163 PHE 0.021 0.002 PHE A 35 TYR 0.024 0.002 TYR A 309 ARG 0.004 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.449 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 30 average time/residue: 0.1754 time to fit residues: 7.4119 Evaluate side-chains 27 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0768 time to fit residues: 0.9157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 40.0000 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.6602 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 6167 Z= 0.355 Angle : 0.582 7.010 8952 Z= 0.315 Chirality : 0.038 0.204 1070 Planarity : 0.005 0.047 648 Dihedral : 22.302 95.544 2269 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.95 % Allowed : 16.23 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.36 (0.45), residues: 358 helix: 1.91 (0.38), residues: 175 sheet: -0.47 (0.63), residues: 75 loop : 0.45 (0.60), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 349 HIS 0.005 0.001 HIS A 163 PHE 0.021 0.002 PHE A 35 TYR 0.024 0.002 TYR A 309 ARG 0.004 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.370 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 30 average time/residue: 0.1838 time to fit residues: 7.5531 Evaluate side-chains 25 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0872 time to fit residues: 0.6683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 40.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6167 Z= 0.131 Angle : 0.435 5.046 8952 Z= 0.242 Chirality : 0.030 0.126 1070 Planarity : 0.003 0.046 648 Dihedral : 21.954 92.630 2269 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.30 % Allowed : 16.88 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.45), residues: 358 helix: 2.55 (0.37), residues: 175 sheet: 0.02 (0.64), residues: 73 loop : 0.49 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 349 HIS 0.004 0.001 HIS A 279 PHE 0.011 0.001 PHE A 206 TYR 0.022 0.001 TYR A 309 ARG 0.002 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.469 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.1605 time to fit residues: 6.8756 Evaluate side-chains 29 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0785 time to fit residues: 1.0184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 10.0000 chunk 4 optimal weight: 0.2980 chunk 37 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 45 optimal weight: 40.0000 chunk 41 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6167 Z= 0.186 Angle : 0.456 4.815 8952 Z= 0.253 Chirality : 0.032 0.149 1070 Planarity : 0.004 0.047 648 Dihedral : 21.959 93.345 2269 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.32 % Allowed : 17.86 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.97 (0.46), residues: 358 helix: 2.53 (0.38), residues: 175 sheet: -0.21 (0.63), residues: 75 loop : 0.51 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 349 HIS 0.003 0.001 HIS A 163 PHE 0.020 0.002 PHE A 35 TYR 0.025 0.002 TYR A 309 ARG 0.001 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.416 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 27 average time/residue: 0.1607 time to fit residues: 6.2292 Evaluate side-chains 25 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0525 time to fit residues: 0.5629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 overall best weight: 7.3994 ------------------------------------------------------------------------------- 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: 0.6617 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6167 Z= 0.398 Angle : 0.625 5.681 8952 Z= 0.338 Chirality : 0.040 0.231 1070 Planarity : 0.005 0.048 648 Dihedral : 22.411 96.895 2269 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.32 % Allowed : 18.51 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.44), residues: 358 helix: 1.71 (0.38), residues: 175 sheet: -0.81 (0.63), residues: 70 loop : 0.11 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 349 HIS 0.006 0.002 HIS A 332 PHE 0.025 0.003 PHE A 35 TYR 0.032 0.003 TYR A 309 ARG 0.004 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.451 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.1746 time to fit residues: 6.9500 Evaluate side-chains 26 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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: 0.6574 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6167 Z= 0.225 Angle : 0.501 4.897 8952 Z= 0.276 Chirality : 0.034 0.183 1070 Planarity : 0.004 0.047 648 Dihedral : 22.218 95.826 2269 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.65 % Allowed : 19.16 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.45), residues: 358 helix: 2.07 (0.38), residues: 175 sheet: -0.67 (0.64), residues: 70 loop : 0.19 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 349 HIS 0.004 0.001 HIS A 332 PHE 0.024 0.002 PHE A 93 TYR 0.024 0.002 TYR A 309 ARG 0.002 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.388 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.1654 time to fit residues: 6.6627 Evaluate side-chains 26 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.462 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0610 time to fit residues: 0.6376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 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 = 0.4165 r_free = 0.4165 target = 0.177927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135829 restraints weight = 8560.518| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.67 r_work: 0.3613 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6167 Z= 0.196 Angle : 0.468 4.802 8952 Z= 0.259 Chirality : 0.032 0.157 1070 Planarity : 0.004 0.047 648 Dihedral : 22.090 94.034 2269 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.65 % Allowed : 18.83 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.45), residues: 358 helix: 2.25 (0.38), residues: 175 sheet: -0.38 (0.68), residues: 63 loop : 0.13 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 349 HIS 0.003 0.001 HIS A 163 PHE 0.027 0.002 PHE A 93 TYR 0.024 0.002 TYR A 309 ARG 0.002 0.000 ARG A 38 =============================================================================== Job complete usr+sys time: 1042.51 seconds wall clock time: 19 minutes 55.54 seconds (1195.54 seconds total)