Starting phenix.real_space_refine on Fri Dec 8 06:55:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/12_2023/8qk3_18455.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/12_2023/8qk3_18455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/12_2023/8qk3_18455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/12_2023/8qk3_18455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/12_2023/8qk3_18455.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/12_2023/8qk3_18455.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4754 2.51 5 N 1241 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7535 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "E" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1018 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 113} Chain: "D" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1873 Classifications: {'peptide': 238} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 227} Time building chain proxies: 4.47, per 1000 atoms: 0.59 Number of scatterers: 7535 At special positions: 0 Unit cell: (106.68, 122.64, 96.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1500 8.00 N 1241 7.00 C 4754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 1 " - pdb=" SG CYS E 46 " distance=2.03 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 107 " distance=1.38 Simple disulfide: pdb=" SG CYS E 93 " - pdb=" SG CYS E 123 " distance=2.03 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: 2.99 Conformation dependent library (CDL) restraints added in 1.5 seconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1814 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 6.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 249 through 252 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 246 through 252 removed outlier: 5.413A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 249 through 252 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing sheet with id=AA1, first strand: chain 'B' and resid 133 through 135 Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 199 removed outlier: 5.674A pdb=" N ASN B 297 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 199 removed outlier: 6.272A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA7, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AA8, first strand: chain 'C' and resid 190 through 199 removed outlier: 6.419A pdb=" N ASN C 297 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AB3, first strand: chain 'E' and resid 74 through 78 removed outlier: 3.831A pdb=" N TYR E 87 " --> pdb=" O CYS E 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 97 through 99 Processing sheet with id=AB5, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.739A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.635A pdb=" N ILE D 171 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 222 through 223 removed outlier: 6.766A pdb=" N VAL D 285 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG D 243 " --> pdb=" O GLY D 283 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY D 283 " --> pdb=" O ARG D 243 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 229 through 232 removed outlier: 6.626A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) 212 hydrogen bonds defined for protein. 528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1355 1.32 - 1.45: 2045 1.45 - 1.57: 4240 1.57 - 1.69: 0 1.69 - 1.82: 60 Bond restraints: 7700 Sorted by residual: bond pdb=" C PRO E 4 " pdb=" O PRO E 4 " ideal model delta sigma weight residual 1.240 1.207 0.033 1.12e-02 7.97e+03 8.67e+00 bond pdb=" N TYR E 20 " pdb=" CA TYR E 20 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.24e-02 6.50e+03 7.32e+00 bond pdb=" C PRO E 5 " pdb=" O PRO E 5 " ideal model delta sigma weight residual 1.233 1.202 0.031 1.19e-02 7.06e+03 6.86e+00 bond pdb=" N TRP E 52 " pdb=" CA TRP E 52 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.22e-02 6.72e+03 4.85e+00 bond pdb=" C TYR B 242 " pdb=" N PRO B 243 " ideal model delta sigma weight residual 1.328 1.353 -0.025 1.25e-02 6.40e+03 4.09e+00 ... (remaining 7695 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.13: 248 107.13 - 113.90: 4297 113.90 - 120.67: 2933 120.67 - 127.45: 2944 127.45 - 134.22: 75 Bond angle restraints: 10497 Sorted by residual: angle pdb=" N PRO E 4 " pdb=" CA PRO E 4 " pdb=" C PRO E 4 " ideal model delta sigma weight residual 110.70 105.76 4.94 1.22e+00 6.72e-01 1.64e+01 angle pdb=" N GLU E 2 " pdb=" CA GLU E 2 " pdb=" C GLU E 2 " ideal model delta sigma weight residual 113.89 108.62 5.27 1.58e+00 4.01e-01 1.11e+01 angle pdb=" C GLU E 2 " pdb=" N GLU E 3 " pdb=" CA GLU E 3 " ideal model delta sigma weight residual 122.26 118.69 3.57 1.10e+00 8.26e-01 1.06e+01 angle pdb=" N VAL D 129 " pdb=" CA VAL D 129 " pdb=" C VAL D 129 " ideal model delta sigma weight residual 111.45 108.49 2.96 9.30e-01 1.16e+00 1.01e+01 angle pdb=" N ASN A 278 " pdb=" CA ASN A 278 " pdb=" C ASN A 278 " ideal model delta sigma weight residual 111.30 115.56 -4.26 1.36e+00 5.41e-01 9.83e+00 ... (remaining 10492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4287 17.61 - 35.22: 241 35.22 - 52.83: 52 52.83 - 70.44: 16 70.44 - 88.05: 5 Dihedral angle restraints: 4601 sinusoidal: 1790 harmonic: 2811 Sorted by residual: dihedral pdb=" CA SER A 153 " pdb=" C SER A 153 " pdb=" N ASN A 154 " pdb=" CA ASN A 154 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASN B 154 " pdb=" C ASN B 154 " pdb=" N ASP B 155 " pdb=" CA ASP B 155 " ideal model delta harmonic sigma weight residual 180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA SER B 153 " pdb=" C SER B 153 " pdb=" N ASN B 154 " pdb=" CA ASN B 154 " ideal model delta harmonic sigma weight residual 180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 734 0.031 - 0.062: 315 0.062 - 0.093: 58 0.093 - 0.124: 74 0.124 - 0.155: 20 Chirality restraints: 1201 Sorted by residual: chirality pdb=" CA PRO E 4 " pdb=" N PRO E 4 " pdb=" C PRO E 4 " pdb=" CB PRO E 4 " both_signs ideal model delta sigma weight residual False 2.72 2.87 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE D 324 " pdb=" N ILE D 324 " pdb=" C ILE D 324 " pdb=" CB ILE D 324 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA ASN A 278 " pdb=" N ASN A 278 " pdb=" C ASN A 278 " pdb=" CB ASN A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 1198 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 158 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.14e+00 pdb=" N PRO D 159 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 159 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 159 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 53 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO E 54 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 54 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 54 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 324 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO D 325 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 325 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 325 " 0.027 5.00e-02 4.00e+02 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 58 2.51 - 3.11: 5735 3.11 - 3.71: 11235 3.71 - 4.30: 16926 4.30 - 4.90: 28155 Nonbonded interactions: 62109 Sorted by model distance: nonbonded pdb=" OE1 GLU D 170 " pdb=" OH TYR D 172 " model vdw 1.913 2.440 nonbonded pdb=" O GLU D 120 " pdb=" OG SER D 123 " model vdw 1.931 2.440 nonbonded pdb=" OG1 THR D 280 " pdb=" OE2 GLU D 282 " model vdw 2.075 2.440 nonbonded pdb=" OG SER A 264 " pdb=" OE2 GLU A 303 " model vdw 2.115 2.440 nonbonded pdb=" NZ LYS A 233 " pdb=" OH TYR A 288 " model vdw 2.136 2.520 ... (remaining 62104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.740 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: 3.640 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.310 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.003 0.044 7700 Z= 0.208 Angle : 0.597 6.412 10497 Z= 0.356 Chirality : 0.045 0.155 1201 Planarity : 0.004 0.051 1360 Dihedral : 12.490 88.050 2775 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.12 % Allowed : 12.50 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.49 (0.27), residues: 945 helix: -0.25 (1.26), residues: 21 sheet: -0.33 (0.26), residues: 354 loop : -0.22 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 296 HIS 0.004 0.001 HIS A 218 PHE 0.016 0.001 PHE C 172 TYR 0.012 0.001 TYR D 172 ARG 0.003 0.000 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.2687 time to fit residues: 79.4630 Evaluate side-chains 157 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0720 time to fit residues: 1.3723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 0.0870 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 0.0070 chunk 83 optimal weight: 1.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN E 90 HIS ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7700 Z= 0.236 Angle : 0.634 9.651 10497 Z= 0.335 Chirality : 0.046 0.273 1201 Planarity : 0.004 0.034 1360 Dihedral : 4.768 27.440 1034 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.13 % Allowed : 16.27 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.51 (0.27), residues: 945 helix: 0.13 (1.31), residues: 21 sheet: -0.44 (0.27), residues: 347 loop : -0.20 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 52 HIS 0.002 0.001 HIS A 218 PHE 0.024 0.002 PHE A 182 TYR 0.023 0.002 TYR D 186 ARG 0.009 0.001 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 183 average time/residue: 0.2349 time to fit residues: 55.2696 Evaluate side-chains 171 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 0.938 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.0832 time to fit residues: 4.6524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 30.0000 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN B 305 GLN A 149 ASN ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS E 50 HIS ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.128 7700 Z= 0.714 Angle : 0.800 9.723 10497 Z= 0.424 Chirality : 0.050 0.217 1201 Planarity : 0.005 0.036 1360 Dihedral : 5.683 37.568 1034 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.71 % Allowed : 17.45 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.98 (0.27), residues: 945 helix: -1.12 (0.83), residues: 36 sheet: -0.70 (0.26), residues: 351 loop : -0.49 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 116 HIS 0.015 0.003 HIS E 90 PHE 0.020 0.003 PHE E 85 TYR 0.023 0.002 TYR B 256 ARG 0.007 0.001 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 0.2410 time to fit residues: 45.0482 Evaluate side-chains 135 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0729 time to fit residues: 3.3406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 7700 Z= 0.336 Angle : 0.648 9.232 10497 Z= 0.342 Chirality : 0.045 0.210 1201 Planarity : 0.004 0.036 1360 Dihedral : 5.407 35.346 1034 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.12 % Allowed : 18.63 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.27), residues: 945 helix: -0.79 (0.90), residues: 36 sheet: -0.70 (0.26), residues: 349 loop : -0.35 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 296 HIS 0.009 0.001 HIS E 90 PHE 0.026 0.002 PHE E 91 TYR 0.017 0.002 TYR E 106 ARG 0.008 0.001 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 143 average time/residue: 0.2525 time to fit residues: 46.0861 Evaluate side-chains 129 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1304 time to fit residues: 2.9777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 0.0050 chunk 66 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN C 231 ASN E 49 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7700 Z= 0.260 Angle : 0.631 9.277 10497 Z= 0.328 Chirality : 0.046 0.187 1201 Planarity : 0.004 0.035 1360 Dihedral : 5.216 34.890 1034 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.77 % Allowed : 19.81 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.78 (0.27), residues: 945 helix: -0.74 (0.89), residues: 36 sheet: -0.66 (0.27), residues: 351 loop : -0.30 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 116 HIS 0.008 0.001 HIS E 90 PHE 0.016 0.002 PHE E 85 TYR 0.012 0.001 TYR B 320 ARG 0.008 0.001 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 135 average time/residue: 0.2552 time to fit residues: 44.0635 Evaluate side-chains 126 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0725 time to fit residues: 2.2937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 7700 Z= 0.554 Angle : 0.726 8.862 10497 Z= 0.381 Chirality : 0.047 0.161 1201 Planarity : 0.004 0.038 1360 Dihedral : 5.506 35.020 1034 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.89 % Allowed : 19.22 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.89 (0.27), residues: 945 helix: -0.92 (0.90), residues: 36 sheet: -0.71 (0.26), residues: 351 loop : -0.38 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 116 HIS 0.007 0.002 HIS E 90 PHE 0.025 0.002 PHE E 91 TYR 0.022 0.002 TYR B 256 ARG 0.008 0.001 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 124 average time/residue: 0.2676 time to fit residues: 42.2101 Evaluate side-chains 116 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0735 time to fit residues: 2.4376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7700 Z= 0.213 Angle : 0.651 8.350 10497 Z= 0.338 Chirality : 0.046 0.177 1201 Planarity : 0.004 0.038 1360 Dihedral : 5.197 33.816 1034 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.94 % Allowed : 21.46 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.76 (0.27), residues: 945 helix: -0.94 (0.86), residues: 36 sheet: -0.74 (0.26), residues: 362 loop : -0.18 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 116 HIS 0.006 0.001 HIS E 90 PHE 0.017 0.002 PHE E 91 TYR 0.016 0.001 TYR C 320 ARG 0.009 0.001 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 136 average time/residue: 0.2680 time to fit residues: 46.2940 Evaluate side-chains 116 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0729 time to fit residues: 1.7095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7700 Z= 0.194 Angle : 0.669 9.983 10497 Z= 0.344 Chirality : 0.046 0.179 1201 Planarity : 0.004 0.040 1360 Dihedral : 5.014 31.956 1034 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.83 % Allowed : 21.70 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.59 (0.27), residues: 945 helix: -0.86 (0.89), residues: 36 sheet: -0.71 (0.27), residues: 345 loop : -0.01 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 116 HIS 0.004 0.001 HIS E 90 PHE 0.018 0.002 PHE D 301 TYR 0.015 0.001 TYR C 320 ARG 0.006 0.001 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 0.878 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 127 average time/residue: 0.2588 time to fit residues: 42.0268 Evaluate side-chains 123 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0704 time to fit residues: 1.8514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7700 Z= 0.198 Angle : 0.674 9.420 10497 Z= 0.342 Chirality : 0.045 0.173 1201 Planarity : 0.004 0.042 1360 Dihedral : 4.914 31.001 1034 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.59 % Allowed : 22.41 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.56 (0.27), residues: 945 helix: 0.53 (1.35), residues: 18 sheet: -0.65 (0.27), residues: 345 loop : -0.11 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 116 HIS 0.003 0.001 HIS E 90 PHE 0.015 0.002 PHE E 85 TYR 0.014 0.001 TYR C 320 ARG 0.009 0.001 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 0.931 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 126 average time/residue: 0.2485 time to fit residues: 40.6792 Evaluate side-chains 122 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0727 time to fit residues: 1.7080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7700 Z= 0.315 Angle : 0.708 9.864 10497 Z= 0.362 Chirality : 0.045 0.196 1201 Planarity : 0.004 0.057 1360 Dihedral : 5.090 29.942 1034 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.71 % Allowed : 22.17 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.55 (0.27), residues: 945 helix: -0.50 (0.96), residues: 36 sheet: -0.54 (0.27), residues: 335 loop : -0.14 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 116 HIS 0.003 0.001 HIS E 90 PHE 0.015 0.002 PHE C 199 TYR 0.010 0.001 TYR A 320 ARG 0.008 0.001 ARG D 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 0.879 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 120 average time/residue: 0.2383 time to fit residues: 37.2929 Evaluate side-chains 119 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0754 time to fit residues: 1.9039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** 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 = 0.3493 r_free = 0.3493 target = 0.069335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.044878 restraints weight = 26258.873| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 4.52 r_work: 0.2680 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7700 Z= 0.230 Angle : 0.688 9.812 10497 Z= 0.352 Chirality : 0.045 0.143 1201 Planarity : 0.004 0.050 1360 Dihedral : 5.009 29.595 1034 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 23.23 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.50 (0.27), residues: 945 helix: -0.73 (0.92), residues: 36 sheet: -0.46 (0.27), residues: 335 loop : -0.11 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 116 HIS 0.002 0.001 HIS E 90 PHE 0.013 0.002 PHE E 85 TYR 0.013 0.001 TYR C 320 ARG 0.011 0.001 ARG D 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.80 seconds wall clock time: 41 minutes 9.84 seconds (2469.84 seconds total)