Starting phenix.real_space_refine (version: dev) on Sat Feb 18 13:29:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/02_2023/7cr1_30444_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/02_2023/7cr1_30444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/02_2023/7cr1_30444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/02_2023/7cr1_30444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/02_2023/7cr1_30444_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/02_2023/7cr1_30444_trim_updated.pdb" } resolution = 3.4 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= -0.000 sd= 0.004 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 ARG 75": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8220 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2038 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Chain: "B" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2038 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Chain: "C" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2038 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Chain: "D" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2038 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.15, per 1000 atoms: 0.63 Number of scatterers: 8220 At special positions: 0 Unit cell: (124.722, 124.722, 75.036, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 36 16.00 F 4 9.00 O 1328 8.00 N 1384 7.00 C 5464 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: 3.03 Conformation dependent library (CDL) restraints added in 1.0 seconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 92 through 114 Processing helix chain 'A' and resid 123 through 146 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.667A pdb=" N MET A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 254 Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 328 removed outlier: 3.805A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 92 through 114 Processing helix chain 'B' and resid 123 through 146 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 158 through 164 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.667A pdb=" N MET B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 254 Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 288 through 328 removed outlier: 3.806A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 92 through 114 Processing helix chain 'C' and resid 123 through 146 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.666A pdb=" N MET C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET C 211 " --> pdb=" O ARG C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 229 through 254 Processing helix chain 'C' and resid 264 through 275 Processing helix chain 'C' and resid 288 through 328 removed outlier: 3.806A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 92 through 114 Processing helix chain 'D' and resid 123 through 146 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 167 through 182 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.667A pdb=" N MET D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 229 through 254 Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 328 removed outlier: 3.806A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix 568 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1184 1.31 - 1.43: 2633 1.43 - 1.56: 4579 1.56 - 1.68: 0 1.68 - 1.81: 52 Bond restraints: 8448 Sorted by residual: bond pdb=" C12 GB9 D 801 " pdb=" N2 GB9 D 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C12 GB9 C 801 " pdb=" N2 GB9 C 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" C12 GB9 B 801 " pdb=" N2 GB9 B 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" C12 GB9 A 801 " pdb=" N2 GB9 A 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" C5 GB9 C 801 " pdb=" C8 GB9 C 801 " ideal model delta sigma weight residual 1.386 1.524 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 8443 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.29: 169 107.29 - 113.97: 4766 113.97 - 120.66: 3999 120.66 - 127.34: 2398 127.34 - 134.03: 104 Bond angle restraints: 11436 Sorted by residual: angle pdb=" N ASN D 258 " pdb=" CA ASN D 258 " pdb=" C ASN D 258 " ideal model delta sigma weight residual 109.07 114.91 -5.84 1.61e+00 3.86e-01 1.32e+01 angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" C GLU A 257 " ideal model delta sigma weight residual 111.36 115.28 -3.92 1.09e+00 8.42e-01 1.29e+01 angle pdb=" N ASN B 258 " pdb=" CA ASN B 258 " pdb=" C ASN B 258 " ideal model delta sigma weight residual 109.07 114.86 -5.79 1.61e+00 3.86e-01 1.29e+01 angle pdb=" N ASN C 258 " pdb=" CA ASN C 258 " pdb=" C ASN C 258 " ideal model delta sigma weight residual 109.07 114.86 -5.79 1.61e+00 3.86e-01 1.29e+01 angle pdb=" N GLU C 257 " pdb=" CA GLU C 257 " pdb=" C GLU C 257 " ideal model delta sigma weight residual 111.36 115.28 -3.92 1.09e+00 8.42e-01 1.29e+01 ... (remaining 11431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4188 17.35 - 34.69: 456 34.69 - 52.04: 92 52.04 - 69.38: 20 69.38 - 86.73: 16 Dihedral angle restraints: 4772 sinusoidal: 1876 harmonic: 2896 Sorted by residual: dihedral pdb=" CA ARG D 153 " pdb=" C ARG D 153 " pdb=" N TYR D 154 " pdb=" CA TYR D 154 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ARG A 153 " pdb=" C ARG A 153 " pdb=" N TYR A 154 " pdb=" CA TYR A 154 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ARG B 153 " pdb=" C ARG B 153 " pdb=" N TYR B 154 " pdb=" CA TYR B 154 " ideal model delta harmonic sigma weight residual -180.00 -162.83 -17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 4769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 658 0.030 - 0.060: 397 0.060 - 0.090: 151 0.090 - 0.120: 24 0.120 - 0.150: 18 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CA GLU C 254 " pdb=" N GLU C 254 " pdb=" C GLU C 254 " pdb=" CB GLU C 254 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA GLU D 254 " pdb=" N GLU D 254 " pdb=" C GLU D 254 " pdb=" CB GLU D 254 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA GLU B 254 " pdb=" N GLU B 254 " pdb=" C GLU B 254 " pdb=" CB GLU B 254 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1245 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 284 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO D 285 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 285 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 285 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 284 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO C 285 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 284 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 285 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.018 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 983 2.73 - 3.27: 8946 3.27 - 3.81: 13328 3.81 - 4.36: 15538 4.36 - 4.90: 26138 Nonbonded interactions: 64933 Sorted by model distance: nonbonded pdb=" O THR B 276 " pdb=" OG1 THR B 277 " model vdw 2.185 2.440 nonbonded pdb=" O THR A 276 " pdb=" OG1 THR A 277 " model vdw 2.185 2.440 nonbonded pdb=" O THR C 276 " pdb=" OG1 THR C 277 " model vdw 2.185 2.440 nonbonded pdb=" O THR D 276 " pdb=" OG1 THR D 277 " model vdw 2.186 2.440 nonbonded pdb=" OE1 GLU C 254 " pdb=" N GLN C 286 " model vdw 2.202 2.520 ... (remaining 64928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 6 Type Number sf(0) Gaussians S 36 5.16 5 Cl 4 4.86 5 C 5464 2.51 5 N 1384 2.21 5 O 1328 1.98 5 F 4 1.80 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 3.830 Check model and map are aligned: 0.120 Process input model: 24.210 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.012 0.175 8448 Z= 0.784 Angle : 0.735 6.741 11436 Z= 0.413 Chirality : 0.043 0.150 1248 Planarity : 0.003 0.033 1384 Dihedral : 14.924 86.731 2924 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 26.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: -2.00 (0.24), residues: 984 helix: -0.93 (0.15), residues: 808 sheet: None (None), residues: 0 loop : -2.41 (0.50), residues: 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.887 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2630 time to fit residues: 72.4316 Evaluate side-chains 190 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8448 Z= 0.224 Angle : 0.544 5.199 11436 Z= 0.286 Chirality : 0.038 0.129 1248 Planarity : 0.003 0.028 1384 Dihedral : 4.085 14.561 1124 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 2.99 % 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: 0.79 (0.26), residues: 984 helix: 1.26 (0.17), residues: 824 sheet: None (None), residues: 0 loop : -3.39 (0.45), residues: 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 0.897 Fit side-chains outliers start: 25 outliers final: 16 residues processed: 202 average time/residue: 0.2446 time to fit residues: 64.0418 Evaluate side-chains 198 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0844 time to fit residues: 3.6803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 8448 Z= 0.221 Angle : 0.509 4.563 11436 Z= 0.268 Chirality : 0.037 0.121 1248 Planarity : 0.003 0.032 1384 Dihedral : 3.831 13.187 1124 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 2.63 % 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: 1.78 (0.27), residues: 984 helix: 1.90 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -2.93 (0.46), residues: 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.004 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 174 average time/residue: 0.2207 time to fit residues: 51.6338 Evaluate side-chains 167 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0792 time to fit residues: 2.9327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.0050 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 54 optimal weight: 0.0870 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8448 Z= 0.179 Angle : 0.499 4.887 11436 Z= 0.255 Chirality : 0.035 0.108 1248 Planarity : 0.003 0.029 1384 Dihedral : 3.646 12.366 1124 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 2.15 % 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: 2.29 (0.27), residues: 984 helix: 2.24 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -2.67 (0.47), residues: 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 0.958 Fit side-chains outliers start: 18 outliers final: 2 residues processed: 184 average time/residue: 0.2533 time to fit residues: 60.4888 Evaluate side-chains 158 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0983 time to fit residues: 1.5976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 87 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8448 Z= 0.185 Angle : 0.481 4.748 11436 Z= 0.244 Chirality : 0.034 0.111 1248 Planarity : 0.003 0.028 1384 Dihedral : 3.521 11.738 1124 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.96 % 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: 2.60 (0.27), residues: 984 helix: 2.59 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.64 (0.42), residues: 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 0.911 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 162 average time/residue: 0.2494 time to fit residues: 52.6425 Evaluate side-chains 158 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0739 time to fit residues: 1.7354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.0030 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.5930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8448 Z= 0.176 Angle : 0.471 9.537 11436 Z= 0.238 Chirality : 0.034 0.110 1248 Planarity : 0.003 0.026 1384 Dihedral : 3.412 14.250 1124 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 1.20 % 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: 2.83 (0.27), residues: 984 helix: 2.71 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.36 (0.45), residues: 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 0.919 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 160 average time/residue: 0.2247 time to fit residues: 48.0503 Evaluate side-chains 152 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0867 time to fit residues: 2.1918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 0.0030 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.0670 overall best weight: 0.6132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8448 Z= 0.179 Angle : 0.486 8.299 11436 Z= 0.241 Chirality : 0.034 0.113 1248 Planarity : 0.003 0.025 1384 Dihedral : 3.338 14.304 1124 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 1.20 % 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: 2.87 (0.27), residues: 984 helix: 2.70 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -2.24 (0.48), residues: 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 0.850 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 156 average time/residue: 0.2269 time to fit residues: 47.5462 Evaluate side-chains 154 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0741 time to fit residues: 1.9411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 0.0770 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 0.3980 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8448 Z= 0.171 Angle : 0.475 7.880 11436 Z= 0.238 Chirality : 0.034 0.137 1248 Planarity : 0.003 0.024 1384 Dihedral : 3.291 14.747 1124 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 1.08 % 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: 2.92 (0.27), residues: 984 helix: 2.73 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -2.19 (0.48), residues: 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 0.932 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 158 average time/residue: 0.2438 time to fit residues: 51.0631 Evaluate side-chains 151 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0896 time to fit residues: 1.8747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 89 optimal weight: 0.3980 chunk 58 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8448 Z= 0.184 Angle : 0.477 7.742 11436 Z= 0.238 Chirality : 0.034 0.114 1248 Planarity : 0.003 0.024 1384 Dihedral : 3.272 14.168 1124 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 1.08 % 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: 2.89 (0.27), residues: 984 helix: 2.71 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -2.23 (0.48), residues: 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 0.864 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 146 average time/residue: 0.2409 time to fit residues: 46.6547 Evaluate side-chains 148 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0855 time to fit residues: 2.2740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN C 228 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 8448 Z= 0.256 Angle : 0.512 7.631 11436 Z= 0.260 Chirality : 0.036 0.122 1248 Planarity : 0.003 0.027 1384 Dihedral : 3.364 12.395 1124 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.60 % 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: 2.74 (0.27), residues: 984 helix: 2.60 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -2.26 (0.48), residues: 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.959 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 146 average time/residue: 0.2398 time to fit residues: 46.7704 Evaluate side-chains 144 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0774 time to fit residues: 1.4700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.205834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.160116 restraints weight = 9110.513| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.46 r_work: 0.3289 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8448 Z= 0.163 Angle : 0.472 7.559 11436 Z= 0.234 Chirality : 0.033 0.109 1248 Planarity : 0.003 0.023 1384 Dihedral : 3.258 14.221 1124 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 0.48 % 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: 2.94 (0.27), residues: 984 helix: 2.73 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -2.12 (0.49), residues: 176 =============================================================================== Job complete usr+sys time: 1841.78 seconds wall clock time: 34 minutes 20.47 seconds (2060.47 seconds total)