Starting phenix.real_space_refine on Wed Feb 14 00:55:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/02_2024/7cr1_30444_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/02_2024/7cr1_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_2024/7cr1_30444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/02_2024/7cr1_30444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/02_2024/7cr1_30444_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/02_2024/7cr1_30444_trim_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 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. 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-5238/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: 4.88, per 1000 atoms: 0.59 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: 3.06 Conformation dependent library (CDL) restraints added in 1.7 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: 1.61 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: 2.18 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 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.470 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.800 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 % Allowed : 7.18 % Favored : 92.82 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 269 HIS 0.002 0.001 HIS C 324 PHE 0.020 0.002 PHE C 142 TYR 0.012 0.002 TYR B 154 ARG 0.003 0.000 ARG B 75 *********************** 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 : 0.981 Fit side-chains REVERT: A 76 LYS cc_start: 0.6962 (ptmt) cc_final: 0.6505 (ptmm) REVERT: A 204 GLN cc_start: 0.8762 (mm110) cc_final: 0.8499 (mm110) REVERT: B 76 LYS cc_start: 0.6951 (ptmt) cc_final: 0.6472 (ptmm) REVERT: B 204 GLN cc_start: 0.8757 (mm110) cc_final: 0.8481 (mm110) REVERT: C 204 GLN cc_start: 0.8771 (mm110) cc_final: 0.8491 (mm110) REVERT: D 144 ARG cc_start: 0.6476 (mtt-85) cc_final: 0.6274 (mtt-85) REVERT: D 204 GLN cc_start: 0.8764 (mm110) cc_final: 0.8469 (mm110) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2611 time to fit residues: 71.8521 Evaluate side-chains 189 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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: 6.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7833 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8448 Z= 0.243 Angle : 0.563 5.092 11436 Z= 0.295 Chirality : 0.039 0.133 1248 Planarity : 0.004 0.030 1384 Dihedral : 4.099 14.662 1124 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.99 % Allowed : 13.88 % Favored : 83.13 % 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: 0.78 (0.27), residues: 984 helix: 1.26 (0.17), residues: 824 sheet: None (None), residues: 0 loop : -3.41 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 269 HIS 0.002 0.001 HIS C 328 PHE 0.009 0.001 PHE C 297 TYR 0.015 0.001 TYR B 74 ARG 0.005 0.000 ARG B 210 *********************** 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 219 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 0.966 Fit side-chains REVERT: A 70 ARG cc_start: 0.5927 (tpm170) cc_final: 0.5646 (mmp80) REVERT: C 210 ARG cc_start: 0.8042 (ttt-90) cc_final: 0.7567 (tpt-90) outliers start: 25 outliers final: 19 residues processed: 200 average time/residue: 0.2441 time to fit residues: 63.3108 Evaluate side-chains 200 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 118 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 118 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 263 THR 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: 0.5980 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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: 0.7825 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8448 Z= 0.241 Angle : 0.518 6.097 11436 Z= 0.272 Chirality : 0.037 0.126 1248 Planarity : 0.003 0.031 1384 Dihedral : 3.904 13.693 1124 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.14 % Allowed : 17.11 % Favored : 77.75 % 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: 1.64 (0.27), residues: 984 helix: 1.81 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -2.98 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 146 HIS 0.002 0.001 HIS D 328 PHE 0.012 0.001 PHE B 168 TYR 0.011 0.001 TYR B 74 ARG 0.005 0.001 ARG B 213 *********************** 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 206 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 163 time to evaluate : 0.840 Fit side-chains REVERT: A 70 ARG cc_start: 0.5902 (tpm170) cc_final: 0.5676 (mmp80) REVERT: A 101 LEU cc_start: 0.8775 (mt) cc_final: 0.8519 (tt) REVERT: A 206 LEU cc_start: 0.8415 (mp) cc_final: 0.7851 (mp) REVERT: A 320 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8819 (t) REVERT: B 70 ARG cc_start: 0.5795 (tpm170) cc_final: 0.5591 (mmp80) REVERT: B 101 LEU cc_start: 0.8789 (mt) cc_final: 0.8529 (tt) REVERT: B 206 LEU cc_start: 0.8423 (mp) cc_final: 0.7863 (mp) REVERT: B 320 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8850 (t) REVERT: C 70 ARG cc_start: 0.5844 (tpm170) cc_final: 0.5589 (mmp80) REVERT: C 78 GLN cc_start: 0.7146 (tm-30) cc_final: 0.6944 (tm-30) REVERT: C 101 LEU cc_start: 0.8779 (mt) cc_final: 0.8528 (tt) REVERT: C 206 LEU cc_start: 0.8380 (mp) cc_final: 0.7820 (mp) REVERT: C 320 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8797 (t) REVERT: D 101 LEU cc_start: 0.8774 (mt) cc_final: 0.8512 (tt) REVERT: D 123 GLU cc_start: 0.6660 (tt0) cc_final: 0.6421 (tt0) REVERT: D 206 LEU cc_start: 0.8387 (mp) cc_final: 0.7826 (mp) REVERT: D 320 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8815 (t) outliers start: 43 outliers final: 26 residues processed: 185 average time/residue: 0.2236 time to fit residues: 54.9059 Evaluate side-chains 190 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 0.0040 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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: 0.7767 moved from start: 0.2910 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= 0.169 Angle : 0.488 4.937 11436 Z= 0.250 Chirality : 0.035 0.113 1248 Planarity : 0.003 0.028 1384 Dihedral : 3.664 12.558 1124 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.47 % Allowed : 18.78 % Favored : 77.75 % 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 : -2.70 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 146 HIS 0.002 0.000 HIS D 328 PHE 0.010 0.001 PHE C 168 TYR 0.010 0.001 TYR D 74 ARG 0.005 0.000 ARG C 213 *********************** 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 200 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 0.996 Fit side-chains REVERT: A 70 ARG cc_start: 0.5870 (tpm170) cc_final: 0.5658 (mmp80) REVERT: A 76 LYS cc_start: 0.7164 (ptmt) cc_final: 0.6872 (pttt) REVERT: A 101 LEU cc_start: 0.8711 (mt) cc_final: 0.8345 (tt) REVERT: A 120 LYS cc_start: 0.8616 (tppt) cc_final: 0.7765 (tmmt) REVERT: A 206 LEU cc_start: 0.8388 (mp) cc_final: 0.7836 (mp) REVERT: A 320 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8793 (t) REVERT: B 76 LYS cc_start: 0.7157 (ptmt) cc_final: 0.6857 (pttt) REVERT: B 101 LEU cc_start: 0.8717 (mt) cc_final: 0.8337 (tt) REVERT: B 120 LYS cc_start: 0.8601 (tppt) cc_final: 0.7804 (tmmt) REVERT: B 206 LEU cc_start: 0.8369 (mp) cc_final: 0.7828 (mp) REVERT: C 70 ARG cc_start: 0.5851 (tpm170) cc_final: 0.5624 (mmp80) REVERT: C 76 LYS cc_start: 0.7180 (ptmt) cc_final: 0.6717 (ptmm) REVERT: C 101 LEU cc_start: 0.8748 (mt) cc_final: 0.8375 (tt) REVERT: C 120 LYS cc_start: 0.8587 (tppt) cc_final: 0.7764 (tmmt) REVERT: C 206 LEU cc_start: 0.8396 (mp) cc_final: 0.7853 (mp) REVERT: D 76 LYS cc_start: 0.7185 (ptmt) cc_final: 0.6864 (pttt) REVERT: D 101 LEU cc_start: 0.8738 (mt) cc_final: 0.8374 (tt) REVERT: D 120 LYS cc_start: 0.8605 (tppt) cc_final: 0.7751 (tmmt) REVERT: D 206 LEU cc_start: 0.8377 (mp) cc_final: 0.7834 (mp) outliers start: 29 outliers final: 14 residues processed: 184 average time/residue: 0.2615 time to fit residues: 61.6881 Evaluate side-chains 170 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 259 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 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 C 323 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN D 323 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8448 Z= 0.204 Angle : 0.502 9.003 11436 Z= 0.257 Chirality : 0.035 0.124 1248 Planarity : 0.003 0.030 1384 Dihedral : 3.569 12.176 1124 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.47 % Allowed : 18.66 % Favored : 77.87 % 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: 2.62 (0.27), residues: 984 helix: 2.57 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.49 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 146 HIS 0.002 0.000 HIS D 328 PHE 0.008 0.001 PHE B 297 TYR 0.009 0.001 TYR B 284 ARG 0.004 0.000 ARG B 144 *********************** 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 192 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 1.007 Fit side-chains REVERT: A 70 ARG cc_start: 0.5896 (tpm170) cc_final: 0.5693 (mmp80) REVERT: A 76 LYS cc_start: 0.7194 (ptmt) cc_final: 0.6901 (pttt) REVERT: A 101 LEU cc_start: 0.8679 (mt) cc_final: 0.8341 (tt) REVERT: A 120 LYS cc_start: 0.8609 (tppt) cc_final: 0.7774 (tmmt) REVERT: A 206 LEU cc_start: 0.8402 (mp) cc_final: 0.7866 (mp) REVERT: A 320 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8822 (t) REVERT: B 76 LYS cc_start: 0.7212 (ptmt) cc_final: 0.6926 (pttt) REVERT: B 101 LEU cc_start: 0.8669 (mt) cc_final: 0.8329 (tt) REVERT: B 120 LYS cc_start: 0.8646 (tppt) cc_final: 0.7844 (tmmt) REVERT: B 127 TYR cc_start: 0.6783 (t80) cc_final: 0.6154 (m-80) REVERT: B 206 LEU cc_start: 0.8385 (mp) cc_final: 0.7877 (mp) REVERT: C 70 ARG cc_start: 0.5839 (tpm170) cc_final: 0.5617 (mmp80) REVERT: C 76 LYS cc_start: 0.7158 (ptmt) cc_final: 0.6848 (pttt) REVERT: C 101 LEU cc_start: 0.8704 (mt) cc_final: 0.8366 (tt) REVERT: C 120 LYS cc_start: 0.8616 (tppt) cc_final: 0.7822 (tmmt) REVERT: C 127 TYR cc_start: 0.6778 (t80) cc_final: 0.6152 (m-80) REVERT: C 206 LEU cc_start: 0.8385 (mp) cc_final: 0.7861 (mp) REVERT: D 76 LYS cc_start: 0.7133 (ptmt) cc_final: 0.6848 (pttt) REVERT: D 101 LEU cc_start: 0.8694 (mt) cc_final: 0.8363 (tt) REVERT: D 120 LYS cc_start: 0.8609 (tppt) cc_final: 0.7773 (tmmt) REVERT: D 127 TYR cc_start: 0.6815 (t80) cc_final: 0.6173 (m-80) REVERT: D 206 LEU cc_start: 0.8370 (mp) cc_final: 0.7849 (mp) outliers start: 29 outliers final: 24 residues processed: 178 average time/residue: 0.2421 time to fit residues: 55.9709 Evaluate side-chains 183 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7754 moved from start: 0.3288 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= 0.189 Angle : 0.478 9.553 11436 Z= 0.243 Chirality : 0.034 0.117 1248 Planarity : 0.003 0.031 1384 Dihedral : 3.480 11.635 1124 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.47 % Allowed : 18.78 % Favored : 77.75 % 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 (0.28), residues: 984 helix: 2.64 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -2.08 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 146 HIS 0.002 0.000 HIS D 328 PHE 0.008 0.001 PHE B 316 TYR 0.018 0.001 TYR D 82 ARG 0.005 0.000 ARG B 144 *********************** 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 192 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 0.924 Fit side-chains REVERT: A 70 ARG cc_start: 0.5889 (tpm170) cc_final: 0.5687 (mmp80) REVERT: A 76 LYS cc_start: 0.7302 (ptmt) cc_final: 0.7009 (pttt) REVERT: A 120 LYS cc_start: 0.8585 (tppt) cc_final: 0.7773 (tmmt) REVERT: A 206 LEU cc_start: 0.8382 (mp) cc_final: 0.7877 (mp) REVERT: A 320 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8782 (t) REVERT: B 76 LYS cc_start: 0.7334 (ptmt) cc_final: 0.7044 (pttt) REVERT: B 120 LYS cc_start: 0.8638 (tppt) cc_final: 0.7841 (tmmt) REVERT: B 206 LEU cc_start: 0.8365 (mp) cc_final: 0.7861 (mp) REVERT: C 70 ARG cc_start: 0.5824 (tpm170) cc_final: 0.5618 (mmp80) REVERT: C 76 LYS cc_start: 0.7248 (ptmt) cc_final: 0.6961 (pttt) REVERT: C 120 LYS cc_start: 0.8613 (tppt) cc_final: 0.7825 (tmmt) REVERT: C 127 TYR cc_start: 0.6827 (t80) cc_final: 0.6208 (m-80) REVERT: C 206 LEU cc_start: 0.8372 (mp) cc_final: 0.7854 (mp) REVERT: D 76 LYS cc_start: 0.7179 (ptmt) cc_final: 0.6888 (pttt) REVERT: D 120 LYS cc_start: 0.8614 (tppt) cc_final: 0.7820 (tmmt) REVERT: D 127 TYR cc_start: 0.6833 (t80) cc_final: 0.6195 (m-80) REVERT: D 206 LEU cc_start: 0.8362 (mp) cc_final: 0.7873 (mp) outliers start: 29 outliers final: 20 residues processed: 177 average time/residue: 0.2306 time to fit residues: 53.6704 Evaluate side-chains 172 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 0.0060 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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** C 204 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8448 Z= 0.216 Angle : 0.500 8.672 11436 Z= 0.252 Chirality : 0.035 0.122 1248 Planarity : 0.003 0.028 1384 Dihedral : 3.450 12.149 1124 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.83 % Allowed : 18.54 % Favored : 77.63 % 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: 2.83 (0.28), residues: 984 helix: 2.63 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -1.99 (0.53), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 146 HIS 0.001 0.001 HIS D 328 PHE 0.009 0.001 PHE D 297 TYR 0.018 0.001 TYR A 82 ARG 0.004 0.000 ARG B 144 *********************** 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 186 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 0.967 Fit side-chains REVERT: A 70 ARG cc_start: 0.5879 (tpm170) cc_final: 0.5664 (mmp80) REVERT: A 76 LYS cc_start: 0.7314 (ptmt) cc_final: 0.7017 (pttt) REVERT: A 120 LYS cc_start: 0.8590 (tppt) cc_final: 0.7793 (tmmt) REVERT: A 127 TYR cc_start: 0.6814 (t80) cc_final: 0.6216 (m-80) REVERT: A 206 LEU cc_start: 0.8395 (mp) cc_final: 0.7895 (mp) REVERT: A 320 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8781 (t) REVERT: B 76 LYS cc_start: 0.7355 (ptmt) cc_final: 0.7056 (pttt) REVERT: B 120 LYS cc_start: 0.8617 (tppt) cc_final: 0.7860 (tmmt) REVERT: B 127 TYR cc_start: 0.6842 (t80) cc_final: 0.6229 (m-80) REVERT: B 206 LEU cc_start: 0.8418 (mp) cc_final: 0.7908 (mp) REVERT: C 70 ARG cc_start: 0.5805 (tpm170) cc_final: 0.5583 (mmp80) REVERT: C 76 LYS cc_start: 0.7259 (ptmt) cc_final: 0.6973 (pttt) REVERT: C 120 LYS cc_start: 0.8618 (tppt) cc_final: 0.7835 (tmmt) REVERT: C 127 TYR cc_start: 0.6841 (t80) cc_final: 0.6229 (m-80) REVERT: C 206 LEU cc_start: 0.8368 (mp) cc_final: 0.7862 (mp) REVERT: D 76 LYS cc_start: 0.7241 (ptmt) cc_final: 0.6950 (pttt) REVERT: D 120 LYS cc_start: 0.8619 (tppt) cc_final: 0.7828 (tmmt) REVERT: D 127 TYR cc_start: 0.6820 (t80) cc_final: 0.6214 (m-80) REVERT: D 206 LEU cc_start: 0.8357 (mp) cc_final: 0.7870 (mp) outliers start: 32 outliers final: 23 residues processed: 170 average time/residue: 0.2342 time to fit residues: 52.1804 Evaluate side-chains 176 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.0770 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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** ** 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: 0.7703 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8448 Z= 0.146 Angle : 0.478 10.090 11436 Z= 0.236 Chirality : 0.034 0.294 1248 Planarity : 0.003 0.026 1384 Dihedral : 3.310 13.789 1124 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.63 % Allowed : 19.86 % Favored : 77.51 % 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: 2.98 (0.28), residues: 984 helix: 2.70 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -1.77 (0.54), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 146 HIS 0.002 0.000 HIS D 328 PHE 0.007 0.001 PHE D 240 TYR 0.017 0.001 TYR C 82 ARG 0.005 0.000 ARG B 144 *********************** 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 186 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 0.954 Fit side-chains REVERT: A 70 ARG cc_start: 0.5852 (tpm170) cc_final: 0.5643 (mmp80) REVERT: A 76 LYS cc_start: 0.7351 (ptmt) cc_final: 0.7066 (pttt) REVERT: A 120 LYS cc_start: 0.8611 (tppt) cc_final: 0.7783 (tmmt) REVERT: A 206 LEU cc_start: 0.8332 (mp) cc_final: 0.7875 (mp) REVERT: B 76 LYS cc_start: 0.7375 (ptmt) cc_final: 0.7075 (pttt) REVERT: B 120 LYS cc_start: 0.8647 (tppt) cc_final: 0.7850 (tmmt) REVERT: B 206 LEU cc_start: 0.8324 (mp) cc_final: 0.7873 (mp) REVERT: C 76 LYS cc_start: 0.7324 (ptmt) cc_final: 0.7017 (pttt) REVERT: C 120 LYS cc_start: 0.8624 (tppt) cc_final: 0.7819 (tmmt) REVERT: C 206 LEU cc_start: 0.8304 (mp) cc_final: 0.7844 (mp) REVERT: D 76 LYS cc_start: 0.7318 (ptmt) cc_final: 0.7043 (pttt) REVERT: D 120 LYS cc_start: 0.8622 (tppt) cc_final: 0.7777 (tmmt) REVERT: D 206 LEU cc_start: 0.8303 (mp) cc_final: 0.7848 (mp) outliers start: 22 outliers final: 19 residues processed: 176 average time/residue: 0.2321 time to fit residues: 53.9591 Evaluate side-chains 176 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 241 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.0270 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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** C 204 GLN ** 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: 0.7727 moved from start: 0.3650 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= 0.174 Angle : 0.483 7.932 11436 Z= 0.243 Chirality : 0.036 0.292 1248 Planarity : 0.003 0.029 1384 Dihedral : 3.292 13.782 1124 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.11 % Allowed : 19.62 % Favored : 77.27 % 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: 2.99 (0.28), residues: 984 helix: 2.70 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -1.73 (0.54), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 146 HIS 0.002 0.000 HIS C 328 PHE 0.011 0.001 PHE B 316 TYR 0.017 0.001 TYR A 82 ARG 0.007 0.000 ARG A 213 *********************** 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 185 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 0.974 Fit side-chains REVERT: A 70 ARG cc_start: 0.5901 (tpm170) cc_final: 0.5660 (mmp80) REVERT: A 76 LYS cc_start: 0.7421 (ptmt) cc_final: 0.7123 (pttt) REVERT: A 93 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6868 (t80) REVERT: A 120 LYS cc_start: 0.8617 (tppt) cc_final: 0.7787 (tmmt) REVERT: A 206 LEU cc_start: 0.8322 (mp) cc_final: 0.7859 (mp) REVERT: B 76 LYS cc_start: 0.7415 (ptmt) cc_final: 0.7116 (pttt) REVERT: B 93 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6839 (t80) REVERT: B 120 LYS cc_start: 0.8636 (tppt) cc_final: 0.7853 (tmmt) REVERT: B 206 LEU cc_start: 0.8327 (mp) cc_final: 0.7873 (mp) REVERT: C 76 LYS cc_start: 0.7331 (ptmt) cc_final: 0.7041 (pttt) REVERT: C 93 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6832 (t80) REVERT: C 120 LYS cc_start: 0.8634 (tppt) cc_final: 0.7835 (tmmt) REVERT: C 127 TYR cc_start: 0.6911 (t80) cc_final: 0.6241 (m-80) REVERT: C 206 LEU cc_start: 0.8308 (mp) cc_final: 0.7839 (mp) REVERT: D 76 LYS cc_start: 0.7363 (ptmt) cc_final: 0.7078 (pttt) REVERT: D 120 LYS cc_start: 0.8632 (tppt) cc_final: 0.7792 (tmmt) REVERT: D 127 TYR cc_start: 0.6862 (t80) cc_final: 0.6203 (m-80) REVERT: D 206 LEU cc_start: 0.8379 (mp) cc_final: 0.7894 (mp) outliers start: 26 outliers final: 19 residues processed: 174 average time/residue: 0.2439 time to fit residues: 55.0299 Evaluate side-chains 175 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 61 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.0770 chunk 84 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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** ** 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: 0.7706 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8448 Z= 0.162 Angle : 0.504 11.244 11436 Z= 0.247 Chirality : 0.036 0.361 1248 Planarity : 0.003 0.027 1384 Dihedral : 3.248 13.466 1124 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.63 % Allowed : 20.45 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.27), residues: 984 helix: 2.66 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -1.74 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 146 HIS 0.002 0.000 HIS A 328 PHE 0.009 0.001 PHE B 316 TYR 0.017 0.001 TYR D 82 ARG 0.006 0.000 ARG A 213 ********************** 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 183 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 0.992 Fit side-chains REVERT: A 70 ARG cc_start: 0.5847 (tpm170) cc_final: 0.5581 (mmp80) REVERT: A 76 LYS cc_start: 0.7378 (ptmt) cc_final: 0.7101 (pttt) REVERT: A 93 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6819 (t80) REVERT: A 120 LYS cc_start: 0.8617 (tppt) cc_final: 0.7784 (tmmt) REVERT: A 206 LEU cc_start: 0.8305 (mp) cc_final: 0.7853 (mp) REVERT: B 76 LYS cc_start: 0.7324 (ptmt) cc_final: 0.7029 (pttt) REVERT: B 93 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6835 (t80) REVERT: B 120 LYS cc_start: 0.8646 (tppt) cc_final: 0.7855 (tmmt) REVERT: B 206 LEU cc_start: 0.8292 (mp) cc_final: 0.7844 (mp) REVERT: C 76 LYS cc_start: 0.7355 (ptmt) cc_final: 0.7064 (pttt) REVERT: C 93 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6790 (t80) REVERT: C 120 LYS cc_start: 0.8679 (tppt) cc_final: 0.7852 (tmmt) REVERT: C 127 TYR cc_start: 0.6841 (t80) cc_final: 0.6165 (m-80) REVERT: C 206 LEU cc_start: 0.8274 (mp) cc_final: 0.7818 (mp) REVERT: D 76 LYS cc_start: 0.7386 (ptmt) cc_final: 0.7092 (pttt) REVERT: D 120 LYS cc_start: 0.8612 (tppt) cc_final: 0.7792 (tmmt) REVERT: D 127 TYR cc_start: 0.6819 (t80) cc_final: 0.6155 (m-80) REVERT: D 206 LEU cc_start: 0.8341 (mp) cc_final: 0.7870 (mp) outliers start: 22 outliers final: 18 residues processed: 173 average time/residue: 0.2478 time to fit residues: 55.9762 Evaluate side-chains 179 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 22 optimal weight: 0.3980 chunk 79 optimal weight: 0.0060 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.0470 chunk 57 optimal weight: 0.3980 overall best weight: 0.1892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN B 78 GLN C 78 GLN C 204 GLN D 78 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.215448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.171144 restraints weight = 9327.238| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.09 r_work: 0.3452 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8448 Z= 0.145 Angle : 0.491 10.296 11436 Z= 0.238 Chirality : 0.035 0.344 1248 Planarity : 0.003 0.056 1384 Dihedral : 3.148 13.975 1124 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.27 % Allowed : 21.05 % Favored : 76.67 % 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 (0.27), residues: 984 helix: 2.64 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -1.59 (0.53), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 146 HIS 0.002 0.000 HIS A 328 PHE 0.011 0.001 PHE A 168 TYR 0.017 0.001 TYR C 82 ARG 0.008 0.000 ARG D 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2003.13 seconds wall clock time: 36 minutes 58.40 seconds (2218.40 seconds total)