Starting phenix.real_space_refine (version: dev) on Fri Feb 17 09:44:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/02_2023/5ms1_3562.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/02_2023/5ms1_3562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/02_2023/5ms1_3562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/02_2023/5ms1_3562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/02_2023/5ms1_3562.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/02_2023/5ms1_3562.pdb" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 4350 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1501 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 170} Chain breaks: 1 Chain: "B" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2849 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Time building chain proxies: 3.04, per 1000 atoms: 0.70 Number of scatterers: 4350 At special positions: 0 Unit cell: (89.1, 85.8, 91.3, 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 30 16.00 O 814 8.00 N 732 7.00 C 2774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 664.1 milliseconds 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1034 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 12.9% alpha, 46.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 58 through 63 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.522A pdb=" N ASP B 321 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.226A pdb=" N MET A 163 " --> pdb=" O PRO A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.226A pdb=" N MET A 163 " --> pdb=" O PRO A 13 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA A 63 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN A 174 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 41 removed outlier: 3.734A pdb=" N ARG A 106 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 32 removed outlier: 6.017A pdb=" N LYS B 24 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 172 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 46 removed outlier: 5.691A pdb=" N VAL B 41 " --> pdb=" O CYS B 152 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS B 152 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS B 87 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 111 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 202 removed outlier: 7.015A pdb=" N CYS B 187 " --> pdb=" O CYS B 355 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N CYS B 355 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 189 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 349 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG B 195 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS B 347 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N MET B 197 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N GLY B 345 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N LYS B 199 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN B 343 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL B 346 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR B 251 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU B 348 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU B 249 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE B 354 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG B 243 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY B 356 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 241 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 202 removed outlier: 7.015A pdb=" N CYS B 187 " --> pdb=" O CYS B 355 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N CYS B 355 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 189 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 349 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG B 195 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS B 347 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N MET B 197 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N GLY B 345 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N LYS B 199 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN B 343 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL B 346 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR B 251 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU B 348 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU B 249 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE B 354 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG B 243 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY B 356 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 241 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 214 179 hydrogen bonds defined for protein. 447 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: 1.63 Time building geometry restraints manager: 1.98 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: 1009 1.32 - 1.45: 1181 1.45 - 1.57: 2226 1.57 - 1.69: 0 1.69 - 1.82: 47 Bond restraints: 4463 Sorted by residual: bond pdb=" N PRO B 282 " pdb=" CA PRO B 282 " ideal model delta sigma weight residual 1.467 1.415 0.052 1.21e-02 6.83e+03 1.83e+01 bond pdb=" N PRO A 181 " pdb=" CA PRO A 181 " ideal model delta sigma weight residual 1.466 1.418 0.048 1.19e-02 7.06e+03 1.59e+01 bond pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 1.466 1.420 0.045 1.19e-02 7.06e+03 1.44e+01 bond pdb=" N PRO A 13 " pdb=" CA PRO A 13 " ideal model delta sigma weight residual 1.467 1.421 0.046 1.21e-02 6.83e+03 1.44e+01 bond pdb=" N PRO B 214 " pdb=" CA PRO B 214 " ideal model delta sigma weight residual 1.467 1.423 0.044 1.21e-02 6.83e+03 1.34e+01 ... (remaining 4458 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.38: 119 105.38 - 112.51: 2197 112.51 - 119.64: 1503 119.64 - 126.77: 2200 126.77 - 133.90: 55 Bond angle restraints: 6074 Sorted by residual: angle pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" O ARG A 77 " ideal model delta sigma weight residual 120.71 113.89 6.82 1.06e+00 8.90e-01 4.15e+01 angle pdb=" C PRO A 20 " pdb=" N PRO A 21 " pdb=" CA PRO A 21 " ideal model delta sigma weight residual 120.03 126.37 -6.34 9.90e-01 1.02e+00 4.10e+01 angle pdb=" C GLY A 126 " pdb=" N PRO A 127 " pdb=" CA PRO A 127 " ideal model delta sigma weight residual 119.64 125.65 -6.01 1.01e+00 9.80e-01 3.54e+01 angle pdb=" C PRO A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta sigma weight residual 119.32 125.73 -6.41 1.14e+00 7.69e-01 3.17e+01 angle pdb=" C THR A 19 " pdb=" N PRO A 20 " pdb=" CA PRO A 20 " ideal model delta sigma weight residual 119.66 123.52 -3.86 7.30e-01 1.88e+00 2.79e+01 ... (remaining 6069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 2555 16.74 - 33.48: 41 33.48 - 50.22: 15 50.22 - 66.96: 9 66.96 - 83.70: 4 Dihedral angle restraints: 2624 sinusoidal: 1022 harmonic: 1602 Sorted by residual: dihedral pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta harmonic sigma weight residual 0.00 37.92 -37.92 0 5.00e+00 4.00e-02 5.75e+01 dihedral pdb=" CG ARG A 154 " pdb=" CD ARG A 154 " pdb=" NE ARG A 154 " pdb=" CZ ARG A 154 " ideal model delta sinusoidal sigma weight residual -90.00 -130.34 40.34 2 1.50e+01 4.44e-03 8.94e+00 dihedral pdb=" CA ASP A 166 " pdb=" CB ASP A 166 " pdb=" CG ASP A 166 " pdb=" OD1 ASP A 166 " ideal model delta sinusoidal sigma weight residual -30.00 -80.90 50.90 1 2.00e+01 2.50e-03 8.86e+00 ... (remaining 2621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 410 0.058 - 0.117: 199 0.117 - 0.175: 51 0.175 - 0.234: 12 0.234 - 0.292: 1 Chirality restraints: 673 Sorted by residual: chirality pdb=" CA MET B 231 " pdb=" N MET B 231 " pdb=" C MET B 231 " pdb=" CB MET B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA SER B 309 " pdb=" N SER B 309 " pdb=" C SER B 309 " pdb=" CB SER B 309 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU B 184 " pdb=" N LEU B 184 " pdb=" C LEU B 184 " pdb=" CB LEU B 184 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 670 not shown) Planarity restraints: 782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 77 " 0.059 2.00e-02 2.50e+03 1.20e-01 1.43e+02 pdb=" C ARG A 77 " -0.207 2.00e-02 2.50e+03 pdb=" O ARG A 77 " 0.077 2.00e-02 2.50e+03 pdb=" N GLY A 78 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 47 " -0.036 2.00e-02 2.50e+03 1.74e-02 7.60e+00 pdb=" CG TRP A 47 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 47 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 47 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP A 47 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 47 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 47 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 47 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 47 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 47 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 130 " 0.036 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO B 131 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " 0.031 5.00e-02 4.00e+02 ... (remaining 779 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1966 2.91 - 3.41: 3911 3.41 - 3.91: 7317 3.91 - 4.40: 8459 4.40 - 4.90: 13903 Nonbonded interactions: 35556 Sorted by model distance: nonbonded pdb=" N GLU B 279 " pdb=" OE1 GLU B 279 " model vdw 2.413 2.520 nonbonded pdb=" OG SER B 366 " pdb=" N ARG B 367 " model vdw 2.438 2.520 nonbonded pdb=" O SER A 183 " pdb=" OG1 THR A 184 " model vdw 2.439 2.440 nonbonded pdb=" N GLU A 101 " pdb=" OE1 GLU A 101 " model vdw 2.442 2.520 nonbonded pdb=" OG1 THR B 224 " pdb=" N GLN B 225 " model vdw 2.474 2.520 ... (remaining 35551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2774 2.51 5 N 732 2.21 5 O 814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.490 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: 19.690 Check model and map are aligned: 0.070 Process input model: 16.680 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.014 0.058 4463 Z= 0.906 Angle : 1.510 8.431 6074 Z= 1.007 Chirality : 0.071 0.292 673 Planarity : 0.008 0.120 782 Dihedral : 9.301 83.699 1590 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 1.09 % Allowed : 5.45 % Favored : 93.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.81 (0.34), residues: 550 helix: -3.05 (0.45), residues: 53 sheet: 1.15 (0.36), residues: 192 loop : -1.24 (0.33), residues: 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.669 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1736 time to fit residues: 36.7368 Evaluate side-chains 91 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 119 ASN A 157 GLN B 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 4463 Z= 0.222 Angle : 0.624 7.244 6074 Z= 0.336 Chirality : 0.047 0.172 673 Planarity : 0.005 0.040 782 Dihedral : 4.633 19.740 594 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.00 % Favored : 97.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.26 (0.34), residues: 550 helix: -1.57 (0.68), residues: 48 sheet: 1.02 (0.37), residues: 197 loop : -0.74 (0.32), residues: 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.518 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1370 time to fit residues: 24.1526 Evaluate side-chains 99 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN B 302 GLN B 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 4463 Z= 0.239 Angle : 0.595 6.876 6074 Z= 0.318 Chirality : 0.046 0.154 673 Planarity : 0.005 0.039 782 Dihedral : 4.453 15.593 594 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.09 % Favored : 96.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.32 (0.35), residues: 550 helix: -1.15 (0.70), residues: 47 sheet: 0.83 (0.38), residues: 201 loop : -0.78 (0.33), residues: 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.549 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1278 time to fit residues: 21.1949 Evaluate side-chains 100 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.2980 chunk 36 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 49 optimal weight: 0.0270 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4463 Z= 0.194 Angle : 0.573 6.360 6074 Z= 0.296 Chirality : 0.045 0.140 673 Planarity : 0.004 0.035 782 Dihedral : 4.293 17.048 594 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.91 % Favored : 96.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.30 (0.35), residues: 550 helix: -1.45 (0.69), residues: 48 sheet: 0.96 (0.38), residues: 190 loop : -0.73 (0.33), residues: 312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.520 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1366 time to fit residues: 22.2814 Evaluate side-chains 89 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN B 128 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 4463 Z= 0.368 Angle : 0.655 7.035 6074 Z= 0.343 Chirality : 0.047 0.165 673 Planarity : 0.005 0.045 782 Dihedral : 4.530 16.959 594 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.82 % Favored : 96.00 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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 (0.34), residues: 550 helix: -1.57 (0.64), residues: 53 sheet: 0.75 (0.37), residues: 192 loop : -0.87 (0.33), residues: 305 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.496 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.1573 time to fit residues: 20.7722 Evaluate side-chains 77 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 4463 Z= 0.182 Angle : 0.559 5.293 6074 Z= 0.293 Chirality : 0.045 0.140 673 Planarity : 0.004 0.051 782 Dihedral : 4.294 16.325 594 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.38 (0.35), residues: 550 helix: -1.31 (0.70), residues: 48 sheet: 0.82 (0.38), residues: 192 loop : -0.77 (0.34), residues: 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.464 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1285 time to fit residues: 17.2517 Evaluate side-chains 76 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 4463 Z= 0.302 Angle : 0.614 7.497 6074 Z= 0.317 Chirality : 0.045 0.152 673 Planarity : 0.005 0.053 782 Dihedral : 4.458 16.321 594 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.57 (0.35), residues: 550 helix: -1.49 (0.67), residues: 54 sheet: 0.67 (0.37), residues: 193 loop : -0.85 (0.34), residues: 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.517 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1442 time to fit residues: 19.2030 Evaluate side-chains 75 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4463 Z= 0.208 Angle : 0.574 8.323 6074 Z= 0.298 Chirality : 0.045 0.170 673 Planarity : 0.004 0.054 782 Dihedral : 4.277 14.729 594 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.65 (0.35), residues: 550 helix: -1.39 (0.70), residues: 48 sheet: 0.73 (0.38), residues: 184 loop : -1.00 (0.34), residues: 318 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.479 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1544 time to fit residues: 18.2506 Evaluate side-chains 67 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN B 189 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 4463 Z= 0.427 Angle : 0.712 8.234 6074 Z= 0.369 Chirality : 0.048 0.167 673 Planarity : 0.005 0.056 782 Dihedral : 4.804 17.139 594 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.91 (0.35), residues: 550 helix: -1.72 (0.63), residues: 53 sheet: 0.45 (0.37), residues: 191 loop : -1.09 (0.34), residues: 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.449 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1762 time to fit residues: 18.1789 Evaluate side-chains 60 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.523 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.6983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4463 Z= 0.172 Angle : 0.564 5.284 6074 Z= 0.298 Chirality : 0.045 0.165 673 Planarity : 0.005 0.056 782 Dihedral : 4.350 16.086 594 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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 (0.35), residues: 550 helix: -1.84 (0.62), residues: 54 sheet: 0.34 (0.37), residues: 187 loop : -0.94 (0.35), residues: 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.510 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1741 time to fit residues: 22.2391 Evaluate side-chains 74 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 1 optimal weight: 0.0370 chunk 34 optimal weight: 10.0000 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.109075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.098058 restraints weight = 6762.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.099209 restraints weight = 5157.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.100140 restraints weight = 4235.662| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4463 Z= 0.153 Angle : 0.566 8.251 6074 Z= 0.292 Chirality : 0.045 0.166 673 Planarity : 0.004 0.056 782 Dihedral : 4.133 14.826 594 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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 (0.35), residues: 550 helix: -1.55 (0.70), residues: 48 sheet: 0.43 (0.38), residues: 188 loop : -0.94 (0.35), residues: 314 =============================================================================== Job complete usr+sys time: 1418.31 seconds wall clock time: 26 minutes 20.85 seconds (1580.85 seconds total)