Starting phenix.real_space_refine on Thu Nov 14 11:43:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pds_17620/11_2024/8pds_17620.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pds_17620/11_2024/8pds_17620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pds_17620/11_2024/8pds_17620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pds_17620/11_2024/8pds_17620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pds_17620/11_2024/8pds_17620.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pds_17620/11_2024/8pds_17620.cif" } resolution = 2.9 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= 0.025 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 26 5.16 5 C 3776 2.51 5 N 1044 2.21 5 O 1196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6056 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2827 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain: "E" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'RNA': 14} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "C" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2827 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 4.97, per 1000 atoms: 0.82 Number of scatterers: 6056 At special positions: 0 Unit cell: (110.25, 90.3, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 14 15.00 O 1196 8.00 N 1044 7.00 C 3776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 910.7 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 67.1% alpha, 5.1% beta 0 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.636A pdb=" N LEU A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 142 removed outlier: 3.628A pdb=" N VAL A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.646A pdb=" N GLN A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.883A pdb=" N LYS A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 191 removed outlier: 3.795A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.894A pdb=" N ARG A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.719A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.527A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.549A pdb=" N GLN B 13 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 14 " --> pdb=" O ILE B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 14' Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.613A pdb=" N LEU C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.570A pdb=" N VAL C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 156 through 171 removed outlier: 3.910A pdb=" N LYS C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 191 removed outlier: 3.884A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 217 through 233 removed outlier: 3.902A pdb=" N ARG C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 268 removed outlier: 3.651A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.762A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.193A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.803A pdb=" N LEU A 111 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 32 through 35 Processing sheet with id=AA4, first strand: chain 'C' and resid 96 through 104 removed outlier: 7.875A pdb=" N LEU C 111 " --> pdb=" O LEU C 100 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1949 1.34 - 1.46: 815 1.46 - 1.57: 3334 1.57 - 1.69: 27 1.69 - 1.81: 46 Bond restraints: 6171 Sorted by residual: bond pdb=" N ILE B 11 " pdb=" CA ILE B 11 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.53e+00 bond pdb=" CB VAL C 92 " pdb=" CG1 VAL C 92 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB VAL A 92 " pdb=" CG1 VAL A 92 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.45e+00 bond pdb=" CB VAL C 190 " pdb=" CG1 VAL C 190 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.89e+00 bond pdb=" CG LEU C 282 " pdb=" CD2 LEU C 282 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 ... (remaining 6166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 7950 1.17 - 2.35: 360 2.35 - 3.52: 53 3.52 - 4.69: 17 4.69 - 5.87: 4 Bond angle restraints: 8384 Sorted by residual: angle pdb=" CA ILE B 11 " pdb=" C ILE B 11 " pdb=" O ILE B 11 " ideal model delta sigma weight residual 120.47 117.86 2.61 1.08e+00 8.57e-01 5.86e+00 angle pdb=" C LEU C 52 " pdb=" N TYR C 53 " pdb=" CA TYR C 53 " ideal model delta sigma weight residual 122.60 118.83 3.77 1.56e+00 4.11e-01 5.83e+00 angle pdb=" C LEU A 52 " pdb=" N TYR A 53 " pdb=" CA TYR A 53 " ideal model delta sigma weight residual 122.65 119.02 3.63 1.60e+00 3.91e-01 5.14e+00 angle pdb=" N ILE C 51 " pdb=" CA ILE C 51 " pdb=" C ILE C 51 " ideal model delta sigma weight residual 113.00 110.37 2.63 1.30e+00 5.92e-01 4.10e+00 angle pdb=" N GLN C 216 " pdb=" CA GLN C 216 " pdb=" CB GLN C 216 " ideal model delta sigma weight residual 110.07 112.91 -2.84 1.45e+00 4.76e-01 3.83e+00 ... (remaining 8379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3444 17.57 - 35.15: 281 35.15 - 52.72: 44 52.72 - 70.29: 15 70.29 - 87.87: 25 Dihedral angle restraints: 3809 sinusoidal: 1657 harmonic: 2152 Sorted by residual: dihedral pdb=" CA GLY C 311 " pdb=" C GLY C 311 " pdb=" N LEU C 312 " pdb=" CA LEU C 312 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ILE A 334 " pdb=" C ILE A 334 " pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta harmonic sigma weight residual -180.00 -163.64 -16.36 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ALA C 251 " pdb=" C ALA C 251 " pdb=" N TYR C 252 " pdb=" CA TYR C 252 " ideal model delta harmonic sigma weight residual 180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 598 0.032 - 0.065: 263 0.065 - 0.097: 92 0.097 - 0.129: 28 0.129 - 0.162: 5 Chirality restraints: 986 Sorted by residual: chirality pdb=" CA ILE B 11 " pdb=" N ILE B 11 " pdb=" C ILE B 11 " pdb=" CB ILE B 11 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA VAL C 119 " pdb=" N VAL C 119 " pdb=" C VAL C 119 " pdb=" CB VAL C 119 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 983 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C E 66 " -0.021 2.00e-02 2.50e+03 1.11e-02 2.76e+00 pdb=" N1 C E 66 " 0.024 2.00e-02 2.50e+03 pdb=" C2 C E 66 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C E 66 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C E 66 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C E 66 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C E 66 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C E 66 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C E 66 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 53 " -0.006 2.00e-02 2.50e+03 1.11e-02 2.46e+00 pdb=" CG TYR C 53 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C 53 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 53 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C 53 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 53 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 53 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 53 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 73 " -0.020 2.00e-02 2.50e+03 1.02e-02 2.33e+00 pdb=" N1 C E 73 " 0.021 2.00e-02 2.50e+03 pdb=" C2 C E 73 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C E 73 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C E 73 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C E 73 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C E 73 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C E 73 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C E 73 " 0.002 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1066 2.76 - 3.30: 5996 3.30 - 3.83: 10436 3.83 - 4.37: 12651 4.37 - 4.90: 20723 Nonbonded interactions: 50872 Sorted by model distance: nonbonded pdb=" OH TYR A 338 " pdb=" OP2 C E 74 " model vdw 2.230 3.040 nonbonded pdb=" O LEU A 18 " pdb=" OG SER C 233 " model vdw 2.262 3.040 nonbonded pdb=" OG SER A 307 " pdb=" O SER C 235 " model vdw 2.262 3.040 nonbonded pdb=" OP2 C E 67 " pdb=" OH TYR C 338 " model vdw 2.266 3.040 nonbonded pdb=" O2 C E 71 " pdb=" ND2 ASN C 246 " model vdw 2.315 3.120 ... (remaining 50867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 4.850 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.860 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.004 0.055 6171 Z= 0.284 Angle : 0.580 5.865 8384 Z= 0.331 Chirality : 0.042 0.162 986 Planarity : 0.004 0.028 1018 Dihedral : 15.092 87.867 2429 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % 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: -0.16 (0.30), residues: 736 helix: 0.32 (0.24), residues: 474 sheet: -1.22 (0.64), residues: 42 loop : -0.54 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 123 HIS 0.004 0.001 HIS C 56 PHE 0.016 0.002 PHE C 169 TYR 0.025 0.002 TYR C 53 ARG 0.007 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.666 Fit side-chains REVERT: C 135 MET cc_start: 0.8191 (ttm) cc_final: 0.7928 (ttm) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 1.7335 time to fit residues: 176.0008 Evaluate side-chains 82 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 18 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6171 Z= 0.258 Angle : 0.540 5.788 8384 Z= 0.288 Chirality : 0.041 0.141 986 Planarity : 0.004 0.033 1018 Dihedral : 11.621 74.596 1031 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.74 % Allowed : 8.04 % Favored : 90.22 % 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: 0.46 (0.30), residues: 736 helix: 0.85 (0.24), residues: 478 sheet: -1.08 (0.64), residues: 42 loop : -0.43 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 123 HIS 0.004 0.001 HIS C 56 PHE 0.014 0.002 PHE C 169 TYR 0.015 0.002 TYR C 69 ARG 0.006 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.742 Fit side-chains REVERT: A 26 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7740 (mtmm) REVERT: A 105 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7269 (p0) REVERT: A 208 ARG cc_start: 0.7743 (tpt-90) cc_final: 0.7360 (tpm-80) REVERT: C 272 MET cc_start: 0.8025 (mmm) cc_final: 0.7788 (mmm) REVERT: C 283 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7437 (mmpt) outliers start: 11 outliers final: 7 residues processed: 88 average time/residue: 1.6189 time to fit residues: 147.9103 Evaluate side-chains 87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 66 optimal weight: 0.0070 chunk 71 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 53 optimal weight: 0.0980 overall best weight: 0.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 284 GLN C 150 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6171 Z= 0.129 Angle : 0.454 6.986 8384 Z= 0.243 Chirality : 0.037 0.137 986 Planarity : 0.003 0.033 1018 Dihedral : 11.522 73.758 1031 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.58 % Allowed : 10.09 % Favored : 88.33 % 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: 1.19 (0.31), residues: 736 helix: 1.47 (0.24), residues: 478 sheet: -0.87 (0.67), residues: 42 loop : -0.25 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 123 HIS 0.002 0.001 HIS A 15 PHE 0.007 0.001 PHE C 224 TYR 0.010 0.001 TYR A 53 ARG 0.007 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7676 (tpt-90) cc_final: 0.7315 (tpm-80) REVERT: C 283 LYS cc_start: 0.7932 (pptt) cc_final: 0.7399 (mmpt) outliers start: 10 outliers final: 5 residues processed: 86 average time/residue: 1.5563 time to fit residues: 139.3700 Evaluate side-chains 82 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 66 optimal weight: 0.0570 chunk 70 optimal weight: 0.0870 chunk 63 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6171 Z= 0.223 Angle : 0.496 6.406 8384 Z= 0.261 Chirality : 0.039 0.129 986 Planarity : 0.004 0.036 1018 Dihedral : 11.464 74.434 1031 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.52 % Allowed : 10.41 % Favored : 87.07 % 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: 1.07 (0.31), residues: 736 helix: 1.37 (0.24), residues: 478 sheet: -0.95 (0.66), residues: 42 loop : -0.28 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 123 HIS 0.003 0.001 HIS C 56 PHE 0.014 0.002 PHE C 169 TYR 0.014 0.002 TYR C 69 ARG 0.008 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7728 (mtmm) REVERT: A 208 ARG cc_start: 0.7712 (tpt-90) cc_final: 0.7341 (tpm-80) REVERT: C 249 MET cc_start: 0.8978 (mmp) cc_final: 0.8771 (mmt) REVERT: C 283 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7439 (mmpt) outliers start: 16 outliers final: 11 residues processed: 92 average time/residue: 1.5265 time to fit residues: 146.1861 Evaluate side-chains 94 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 360 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN C 150 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6171 Z= 0.274 Angle : 0.535 6.908 8384 Z= 0.283 Chirality : 0.041 0.136 986 Planarity : 0.004 0.037 1018 Dihedral : 11.480 74.634 1031 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.31 % Allowed : 11.51 % Favored : 85.17 % 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: 0.82 (0.30), residues: 736 helix: 1.17 (0.24), residues: 478 sheet: -1.04 (0.65), residues: 42 loop : -0.36 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 123 HIS 0.003 0.001 HIS C 56 PHE 0.016 0.002 PHE C 169 TYR 0.016 0.002 TYR C 69 ARG 0.010 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7734 (tpt-90) cc_final: 0.7347 (tpm-80) REVERT: C 216 GLN cc_start: 0.7757 (mt0) cc_final: 0.7550 (mp10) REVERT: C 341 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7305 (ptm-80) outliers start: 21 outliers final: 14 residues processed: 91 average time/residue: 1.4624 time to fit residues: 138.7475 Evaluate side-chains 94 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 360 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6171 Z= 0.378 Angle : 0.602 6.976 8384 Z= 0.316 Chirality : 0.044 0.141 986 Planarity : 0.004 0.041 1018 Dihedral : 11.496 75.094 1031 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.31 % Allowed : 11.83 % Favored : 84.86 % 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: 0.42 (0.30), residues: 736 helix: 0.86 (0.23), residues: 478 sheet: -1.19 (0.65), residues: 42 loop : -0.52 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 123 HIS 0.003 0.001 HIS C 56 PHE 0.020 0.002 PHE C 169 TYR 0.018 0.002 TYR C 69 ARG 0.011 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.4424 (p90) REVERT: A 208 ARG cc_start: 0.7755 (tpt-90) cc_final: 0.7376 (tpm-80) REVERT: C 216 GLN cc_start: 0.7768 (mt0) cc_final: 0.7462 (tp40) REVERT: C 341 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7142 (ptm-80) outliers start: 21 outliers final: 14 residues processed: 92 average time/residue: 1.5147 time to fit residues: 145.4718 Evaluate side-chains 94 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 360 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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: 0.8022 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6171 Z= 0.233 Angle : 0.535 7.099 8384 Z= 0.283 Chirality : 0.040 0.140 986 Planarity : 0.004 0.046 1018 Dihedral : 11.499 74.558 1031 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.31 % Allowed : 12.78 % Favored : 83.91 % 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: 0.75 (0.30), residues: 736 helix: 1.13 (0.24), residues: 478 sheet: -1.12 (0.66), residues: 42 loop : -0.41 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 123 HIS 0.002 0.001 HIS C 56 PHE 0.013 0.002 PHE C 169 TYR 0.013 0.002 TYR C 69 ARG 0.012 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7728 (tpt-90) cc_final: 0.7348 (tpm-80) REVERT: C 216 GLN cc_start: 0.7757 (mt0) cc_final: 0.7453 (tp40) REVERT: C 341 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7124 (ptm-80) REVERT: C 363 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7431 (mtpt) outliers start: 21 outliers final: 15 residues processed: 91 average time/residue: 1.4612 time to fit residues: 138.8667 Evaluate side-chains 94 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 360 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6171 Z= 0.263 Angle : 0.551 7.037 8384 Z= 0.290 Chirality : 0.041 0.138 986 Planarity : 0.004 0.052 1018 Dihedral : 11.473 74.622 1031 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.68 % Allowed : 14.20 % Favored : 83.12 % 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: 0.72 (0.30), residues: 736 helix: 1.11 (0.24), residues: 478 sheet: -1.12 (0.66), residues: 42 loop : -0.43 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 123 HIS 0.002 0.001 HIS C 56 PHE 0.015 0.002 PHE C 169 TYR 0.015 0.002 TYR C 69 ARG 0.013 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7735 (tpt-90) cc_final: 0.7352 (tpm-80) REVERT: A 282 LEU cc_start: 0.8629 (mm) cc_final: 0.8363 (mp) REVERT: C 216 GLN cc_start: 0.7754 (mt0) cc_final: 0.7432 (tp40) REVERT: C 283 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7739 (pptt) REVERT: C 341 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7069 (ptm-80) REVERT: C 363 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7400 (mtpt) outliers start: 17 outliers final: 15 residues processed: 88 average time/residue: 1.2584 time to fit residues: 115.2045 Evaluate side-chains 97 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 360 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.8980 chunk 67 optimal weight: 0.0010 chunk 39 optimal weight: 0.0570 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 0.0770 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: