Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 15:31:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm0_21846/08_2023/6wm0_21846.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm0_21846/08_2023/6wm0_21846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm0_21846/08_2023/6wm0_21846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm0_21846/08_2023/6wm0_21846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm0_21846/08_2023/6wm0_21846.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm0_21846/08_2023/6wm0_21846.pdb" } resolution = 3.52 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 5 8.98 5 S 14 5.16 5 C 2740 2.51 5 N 666 2.21 5 O 680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 150": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 4105 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2050 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 9, 'TRANS': 245} Chain: "B" Number of atoms: 2050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2050 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 9, 'TRANS': 245} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.57, per 1000 atoms: 0.63 Number of scatterers: 4105 At special positions: 0 Unit cell: (62.535, 76.179, 94.371, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 5 19.00 S 14 16.00 O 680 8.00 N 666 7.00 C 2740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS B 51 " 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: 1.85 Conformation dependent library (CDL) restraints added in 645.6 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 8 through 27 removed outlier: 4.341A pdb=" N PHE A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 49 Processing helix chain 'A' and resid 53 through 69 removed outlier: 3.765A pdb=" N LYS A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.815A pdb=" N ALA A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 152 removed outlier: 3.821A pdb=" N VAL A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.737A pdb=" N THR A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.724A pdb=" N VAL A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 Processing helix chain 'A' and resid 222 through 260 removed outlier: 4.343A pdb=" N LYS A 257 " --> pdb=" O HIS A 253 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 49 removed outlier: 4.043A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Proline residue: B 29 - end of helix removed outlier: 3.615A pdb=" N LEU B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 71 removed outlier: 3.593A pdb=" N ALA B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 97 removed outlier: 3.523A pdb=" N ILE B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 152 removed outlier: 3.867A pdb=" N VAL B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Proline residue: B 124 - end of helix removed outlier: 3.694A pdb=" N THR B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.722A pdb=" N VAL B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 Processing helix chain 'B' and resid 222 through 260 removed outlier: 3.731A pdb=" N LYS B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS B 257 " --> pdb=" O HIS B 253 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 909 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: 1.12 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1221 1.34 - 1.46: 926 1.46 - 1.57: 2061 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4228 Sorted by residual: bond pdb=" CG1 ILE A 12 " pdb=" CD1 ILE A 12 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.96e-01 bond pdb=" C PRO A 178 " pdb=" N PRO A 179 " ideal model delta sigma weight residual 1.333 1.346 -0.013 1.44e-02 4.82e+03 8.38e-01 bond pdb=" C GLU B 28 " pdb=" N PRO B 29 " ideal model delta sigma weight residual 1.335 1.348 -0.012 1.36e-02 5.41e+03 8.31e-01 bond pdb=" CA VAL A 213 " pdb=" CB VAL A 213 " ideal model delta sigma weight residual 1.533 1.544 -0.011 1.26e-02 6.30e+03 7.74e-01 bond pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " ideal model delta sigma weight residual 1.808 1.780 0.028 3.30e-02 9.18e+02 7.29e-01 ... (remaining 4223 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.34: 141 107.34 - 114.01: 2380 114.01 - 120.69: 1909 120.69 - 127.36: 1262 127.36 - 134.04: 64 Bond angle restraints: 5756 Sorted by residual: angle pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" C VAL A 25 " ideal model delta sigma weight residual 112.96 109.38 3.58 1.00e+00 1.00e+00 1.28e+01 angle pdb=" N PRO B 178 " pdb=" CA PRO B 178 " pdb=" C PRO B 178 " ideal model delta sigma weight residual 110.70 113.86 -3.16 1.22e+00 6.72e-01 6.73e+00 angle pdb=" N PRO A 178 " pdb=" CA PRO A 178 " pdb=" C PRO A 178 " ideal model delta sigma weight residual 110.70 113.82 -3.12 1.22e+00 6.72e-01 6.54e+00 angle pdb=" N PHE A 91 " pdb=" CA PHE A 91 " pdb=" C PHE A 91 " ideal model delta sigma weight residual 111.28 109.01 2.27 1.09e+00 8.42e-01 4.34e+00 angle pdb=" N ILE B 96 " pdb=" CA ILE B 96 " pdb=" C ILE B 96 " ideal model delta sigma weight residual 109.34 113.56 -4.22 2.08e+00 2.31e-01 4.12e+00 ... (remaining 5751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 2102 15.57 - 31.14: 224 31.14 - 46.72: 57 46.72 - 62.29: 9 62.29 - 77.86: 5 Dihedral angle restraints: 2397 sinusoidal: 925 harmonic: 1472 Sorted by residual: dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS B 51 " pdb=" CB CYS B 51 " ideal model delta sinusoidal sigma weight residual 93.00 157.47 -64.47 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" N LYS A 42 " pdb=" CA LYS A 42 " pdb=" CB LYS A 42 " pdb=" CG LYS A 42 " ideal model delta sinusoidal sigma weight residual 180.00 -121.51 -58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLU A 187 " pdb=" C GLU A 187 " pdb=" N TRP A 188 " pdb=" CA TRP A 188 " ideal model delta harmonic sigma weight residual 180.00 164.77 15.23 0 5.00e+00 4.00e-02 9.28e+00 ... (remaining 2394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 349 0.024 - 0.047: 148 0.047 - 0.070: 90 0.070 - 0.094: 38 0.094 - 0.117: 13 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA PRO A 179 " pdb=" N PRO A 179 " pdb=" C PRO A 179 " pdb=" CB PRO A 179 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA PRO B 179 " pdb=" N PRO B 179 " pdb=" C PRO B 179 " pdb=" CB PRO B 179 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA VAL A 153 " pdb=" N VAL A 153 " pdb=" C VAL A 153 " pdb=" CB VAL A 153 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.03e-01 ... (remaining 635 not shown) Planarity restraints: 702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 214 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO B 215 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 215 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 215 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 253 " 0.006 2.00e-02 2.50e+03 8.75e-03 1.15e+00 pdb=" CG HIS B 253 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS B 253 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 253 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS B 253 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 253 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 28 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 29 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " 0.015 5.00e-02 4.00e+02 ... (remaining 699 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 1466 2.85 - 3.42: 4842 3.42 - 4.00: 7303 4.00 - 4.57: 10768 4.57 - 5.14: 15086 Nonbonded interactions: 39465 Sorted by model distance: nonbonded pdb=" OG1 THR A 9 " pdb=" NE1 TRP B 129 " model vdw 2.281 2.520 nonbonded pdb=" O LEU A 125 " pdb=" OG1 THR A 128 " model vdw 2.326 2.440 nonbonded pdb=" O ALA B 158 " pdb=" OG1 THR B 161 " model vdw 2.355 2.440 nonbonded pdb=" OE1 GLU A 186 " pdb=" OH TYR A 219 " model vdw 2.373 2.440 nonbonded pdb=" O GLN B 159 " pdb=" OG1 THR B 163 " model vdw 2.392 2.440 ... (remaining 39460 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' and resid 6 through 260) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.060 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.770 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 0.042 4228 Z= 0.221 Angle : 0.585 6.204 5756 Z= 0.350 Chirality : 0.038 0.117 638 Planarity : 0.003 0.029 702 Dihedral : 14.115 77.859 1454 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.35), residues: 506 helix: -0.19 (0.24), residues: 382 sheet: None (None), residues: 0 loop : -1.47 (0.59), residues: 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1880 time to fit residues: 26.3756 Evaluate side-chains 84 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN A 218 ASN B 44 HIS B 77 ASN B 78 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 4228 Z= 0.249 Angle : 0.567 6.153 5756 Z= 0.305 Chirality : 0.043 0.222 638 Planarity : 0.004 0.025 702 Dihedral : 4.411 14.923 550 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.36), residues: 506 helix: 1.17 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.80 (0.56), residues: 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 103 average time/residue: 0.2018 time to fit residues: 25.1358 Evaluate side-chains 93 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0506 time to fit residues: 0.9811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN B 77 ASN B 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 4228 Z= 0.260 Angle : 0.558 6.296 5756 Z= 0.303 Chirality : 0.041 0.123 638 Planarity : 0.004 0.027 702 Dihedral : 4.308 15.619 550 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.38), residues: 506 helix: 1.77 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.26 (0.60), residues: 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 102 average time/residue: 0.1751 time to fit residues: 21.8306 Evaluate side-chains 91 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.461 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0464 time to fit residues: 1.1633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 4228 Z= 0.192 Angle : 0.552 8.340 5756 Z= 0.290 Chirality : 0.044 0.336 638 Planarity : 0.004 0.029 702 Dihedral : 4.120 14.864 550 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.38), residues: 506 helix: 2.13 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.07 (0.60), residues: 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 105 average time/residue: 0.1832 time to fit residues: 23.5898 Evaluate side-chains 86 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0660 time to fit residues: 0.8815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 4228 Z= 0.190 Angle : 0.542 9.780 5756 Z= 0.287 Chirality : 0.041 0.227 638 Planarity : 0.004 0.030 702 Dihedral : 3.962 14.180 550 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.38), residues: 506 helix: 2.39 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.76 (0.62), residues: 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.474 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 97 average time/residue: 0.1917 time to fit residues: 22.9728 Evaluate side-chains 90 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.466 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0680 time to fit residues: 0.8572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 4228 Z= 0.201 Angle : 0.557 11.370 5756 Z= 0.288 Chirality : 0.043 0.316 638 Planarity : 0.004 0.030 702 Dihedral : 3.943 13.717 550 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.39), residues: 506 helix: 2.44 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.16 (0.64), residues: 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 94 average time/residue: 0.1798 time to fit residues: 20.6227 Evaluate side-chains 90 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0543 time to fit residues: 0.8536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.0010 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 4228 Z= 0.190 Angle : 0.568 11.344 5756 Z= 0.289 Chirality : 0.044 0.326 638 Planarity : 0.004 0.030 702 Dihedral : 3.819 13.276 550 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.39), residues: 506 helix: 2.55 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.00 (0.65), residues: 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 98 average time/residue: 0.1786 time to fit residues: 21.5531 Evaluate side-chains 86 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0396 time to fit residues: 0.7012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4228 Z= 0.192 Angle : 0.585 13.335 5756 Z= 0.293 Chirality : 0.044 0.360 638 Planarity : 0.004 0.031 702 Dihedral : 3.787 13.060 550 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.38), residues: 506 helix: 2.62 (0.26), residues: 386 sheet: None (None), residues: 0 loop : 0.03 (0.63), residues: 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 89 average time/residue: 0.1712 time to fit residues: 19.1603 Evaluate side-chains 89 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.477 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0508 time to fit residues: 0.9769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4228 Z= 0.195 Angle : 0.579 12.044 5756 Z= 0.292 Chirality : 0.045 0.374 638 Planarity : 0.004 0.031 702 Dihedral : 3.723 12.869 550 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.38), residues: 506 helix: 2.59 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.33 (0.62), residues: 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1806 time to fit residues: 20.6450 Evaluate side-chains 87 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4228 Z= 0.179 Angle : 0.587 12.264 5756 Z= 0.295 Chirality : 0.044 0.360 638 Planarity : 0.004 0.031 702 Dihedral : 3.670 12.328 550 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.38), residues: 506 helix: 2.65 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.26 (0.63), residues: 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 91 average time/residue: 0.1687 time to fit residues: 19.2310 Evaluate side-chains 90 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0648 time to fit residues: 0.8314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.148418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113506 restraints weight = 6447.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115987 restraints weight = 4062.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117356 restraints weight = 3099.178| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4228 Z= 0.170 Angle : 0.575 11.980 5756 Z= 0.288 Chirality : 0.045 0.386 638 Planarity : 0.004 0.032 702 Dihedral : 3.583 12.705 550 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.38), residues: 506 helix: 2.78 (0.26), residues: 386 sheet: None (None), residues: 0 loop : 0.14 (0.63), residues: 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1123.08 seconds wall clock time: 21 minutes 26.79 seconds (1286.79 seconds total)