Starting phenix.real_space_refine on Mon Mar 11 02:40:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/03_2024/7u15_26278.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/03_2024/7u15_26278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/03_2024/7u15_26278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/03_2024/7u15_26278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/03_2024/7u15_26278.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/03_2024/7u15_26278.pdb" } resolution = 3.0 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 21 5.16 5 C 2178 2.51 5 N 531 2.21 5 O 699 1.98 5 H 3255 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6684 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2172 Classifications: {'peptide': 135} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain: "A" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2172 Classifications: {'peptide': 135} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain: "C" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2172 Classifications: {'peptide': 135} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.73, per 1000 atoms: 0.56 Number of scatterers: 6684 At special positions: 0 Unit cell: (93.183, 114.123, 39.786, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 O 699 8.00 N 531 7.00 C 2178 6.00 H 3255 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 183 " " NAG A 302 " - " ASN A 145 " " NAG A 303 " - " ASN A 151 " " NAG A 304 " - " ASN A 164 " " NAG B 301 " - " ASN B 183 " " NAG B 302 " - " ASN B 145 " " NAG B 303 " - " ASN B 151 " " NAG B 304 " - " ASN B 164 " " NAG C 301 " - " ASN C 183 " " NAG C 302 " - " ASN C 145 " " NAG C 303 " - " ASN C 151 " " NAG C 304 " - " ASN C 164 " Time building additional restraints: 6.04 Conformation dependent library (CDL) restraints added in 684.0 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.773A pdb=" N ASP B 122 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.649A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.475A pdb=" N VAL B 133 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 removed outlier: 6.827A pdb=" N TYR B 143 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.076A pdb=" N LEU B 150 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 158 removed outlier: 6.608A pdb=" N ASN B 156 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 171 removed outlier: 6.542A pdb=" N VAL B 169 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN B 170 " --> pdb=" O PHE C 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.623A pdb=" N THR B 185 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 191 removed outlier: 6.467A pdb=" N LEU B 190 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.381A pdb=" N ILE B 195 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 206 through 207 removed outlier: 7.009A pdb=" N GLU B 206 " --> pdb=" O MET A 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 210 through 212 removed outlier: 6.784A pdb=" N TYR B 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 217 through 219 removed outlier: 6.077A pdb=" N SER B 218 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 224 through 231 removed outlier: 6.833A pdb=" N THR A 231 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL C 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLN B 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 235 through 236 removed outlier: 6.851A pdb=" N THR B 235 " --> pdb=" O TYR A 236 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 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: 2.25 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3255 1.03 - 1.23: 37 1.23 - 1.42: 1399 1.42 - 1.62: 2011 1.62 - 1.81: 36 Bond restraints: 6738 Sorted by residual: bond pdb=" C1 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C1 NAG C 302 " pdb=" O5 NAG C 302 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" CB ASP A 191 " pdb=" CG ASP A 191 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.18e+00 bond pdb=" CB ASP C 191 " pdb=" CG ASP C 191 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.16e+00 ... (remaining 6733 not shown) Histogram of bond angle deviations from ideal: 81.09 - 91.13: 9 91.13 - 101.18: 6 101.18 - 111.22: 7265 111.22 - 121.26: 3348 121.26 - 131.31: 1441 Bond angle restraints: 12069 Sorted by residual: angle pdb=" CG2 THR A 235 " pdb=" CB THR A 235 " pdb=" HB THR A 235 " ideal model delta sigma weight residual 108.00 81.09 26.91 3.00e+00 1.11e-01 8.05e+01 angle pdb=" CG2 THR B 235 " pdb=" CB THR B 235 " pdb=" HB THR B 235 " ideal model delta sigma weight residual 108.00 81.14 26.86 3.00e+00 1.11e-01 8.02e+01 angle pdb=" CG2 THR C 235 " pdb=" CB THR C 235 " pdb=" HB THR C 235 " ideal model delta sigma weight residual 108.00 81.16 26.84 3.00e+00 1.11e-01 8.00e+01 angle pdb=" OG1 THR B 235 " pdb=" CB THR B 235 " pdb=" HB THR B 235 " ideal model delta sigma weight residual 109.00 82.96 26.04 3.00e+00 1.11e-01 7.53e+01 angle pdb=" OG1 THR C 235 " pdb=" CB THR C 235 " pdb=" HB THR C 235 " ideal model delta sigma weight residual 109.00 83.02 25.98 3.00e+00 1.11e-01 7.50e+01 ... (remaining 12064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2815 16.15 - 32.31: 410 32.31 - 48.46: 66 48.46 - 64.61: 54 64.61 - 80.77: 15 Dihedral angle restraints: 3360 sinusoidal: 1929 harmonic: 1431 Sorted by residual: dihedral pdb=" CA ALA A 204 " pdb=" C ALA A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ALA C 204 " pdb=" C ALA C 204 " pdb=" N GLU C 205 " pdb=" CA GLU C 205 " ideal model delta harmonic sigma weight residual 180.00 150.56 29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ALA B 204 " pdb=" C ALA B 204 " pdb=" N GLU B 205 " pdb=" CA GLU B 205 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 3357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 597 0.293 - 0.585: 3 0.585 - 0.878: 0 0.878 - 1.170: 0 1.170 - 1.463: 3 Chirality restraints: 603 Sorted by residual: chirality pdb=" CB THR A 235 " pdb=" CA THR A 235 " pdb=" OG1 THR A 235 " pdb=" CG2 THR A 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.35e+01 chirality pdb=" CB THR B 235 " pdb=" CA THR B 235 " pdb=" OG1 THR B 235 " pdb=" CG2 THR B 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.34e+01 chirality pdb=" CB THR C 235 " pdb=" CA THR C 235 " pdb=" OG1 THR C 235 " pdb=" CG2 THR C 235 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.34e+01 ... (remaining 600 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 145 " -0.037 2.00e-02 2.50e+03 2.83e-02 1.20e+01 pdb=" CG ASN A 145 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN A 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG A 302 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 145 " -0.037 2.00e-02 2.50e+03 2.82e-02 1.19e+01 pdb=" CG ASN C 145 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN C 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG C 302 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 145 " -0.037 2.00e-02 2.50e+03 2.81e-02 1.19e+01 pdb=" CG ASN B 145 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN B 145 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 145 " 0.028 2.00e-02 2.50e+03 pdb="HD21 ASN B 145 " 0.010 2.00e-02 2.50e+03 pdb=" C1 NAG B 302 " -0.037 2.00e-02 2.50e+03 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 483 2.19 - 2.79: 13507 2.79 - 3.40: 17849 3.40 - 4.00: 24411 4.00 - 4.60: 34874 Nonbonded interactions: 91124 Sorted by model distance: nonbonded pdb=" H VAL B 128 " pdb=" O VAL C 128 " model vdw 1.591 1.850 nonbonded pdb=" O VAL B 128 " pdb=" H VAL A 128 " model vdw 1.612 1.850 nonbonded pdb=" OG SER B 240 " pdb=" HH TYR C 236 " model vdw 1.663 1.850 nonbonded pdb=" HH TYR B 236 " pdb=" OG SER A 240 " model vdw 1.680 1.850 nonbonded pdb=" O GLU B 205 " pdb=" H GLU C 206 " model vdw 1.745 1.850 ... (remaining 91119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.100 Extract box with map and model: 3.910 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.440 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 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 : 0.006 0.060 3483 Z= 0.400 Angle : 1.217 11.646 4737 Z= 0.678 Chirality : 0.124 1.463 603 Planarity : 0.009 0.056 573 Dihedral : 17.227 69.314 1461 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.44 % Allowed : 33.86 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -6.51 (0.28), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.21), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS C 239 PHE 0.006 0.001 PHE B 237 TYR 0.028 0.003 TYR A 250 ARG 0.007 0.002 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 ARG cc_start: 0.7214 (ptp90) cc_final: 0.6847 (ttp-110) REVERT: B 207 MET cc_start: 0.5623 (tmt) cc_final: 0.5314 (tmm) REVERT: A 124 LYS cc_start: 0.8111 (tppt) cc_final: 0.6240 (pptt) REVERT: A 180 ARG cc_start: 0.7229 (ptp90) cc_final: 0.6625 (mmm160) REVERT: A 207 MET cc_start: 0.5681 (tmt) cc_final: 0.5338 (tmm) REVERT: C 155 ASN cc_start: 0.7116 (m-40) cc_final: 0.6287 (p0) REVERT: C 180 ARG cc_start: 0.7526 (ptp90) cc_final: 0.6348 (ptp90) REVERT: C 207 MET cc_start: 0.6443 (tmt) cc_final: 0.6016 (tmm) REVERT: C 227 MET cc_start: 0.8210 (mtm) cc_final: 0.7970 (mtm) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 1.4117 time to fit residues: 137.6875 Evaluate side-chains 78 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 250 TYR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN B 242 GLN A 154 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN C 154 ASN C 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3483 Z= 0.212 Angle : 0.734 11.603 4737 Z= 0.407 Chirality : 0.113 1.529 603 Planarity : 0.005 0.054 573 Dihedral : 9.936 59.509 719 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 19.80 % Favored : 79.95 % Rotamer: Outliers : 6.61 % Allowed : 29.89 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -6.23 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.74 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 239 PHE 0.011 0.002 PHE B 213 TYR 0.024 0.002 TYR B 250 ARG 0.003 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 ASN cc_start: 0.7122 (t0) cc_final: 0.6894 (t0) REVERT: B 207 MET cc_start: 0.5956 (tmt) cc_final: 0.5583 (tmm) REVERT: A 124 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.6145 (pptt) REVERT: A 178 LYS cc_start: 0.7413 (ptmm) cc_final: 0.5279 (mmpt) REVERT: A 180 ARG cc_start: 0.7486 (ptp90) cc_final: 0.6826 (mmp-170) REVERT: A 207 MET cc_start: 0.5748 (tmt) cc_final: 0.5372 (tmm) REVERT: A 247 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.5950 (mtp180) REVERT: C 150 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7336 (mt) REVERT: C 180 ARG cc_start: 0.7645 (ptp90) cc_final: 0.6542 (ptt90) REVERT: C 207 MET cc_start: 0.6268 (tmt) cc_final: 0.5808 (tmm) REVERT: C 227 MET cc_start: 0.8542 (mtm) cc_final: 0.8280 (mtm) outliers start: 25 outliers final: 8 residues processed: 93 average time/residue: 1.7117 time to fit residues: 165.5458 Evaluate side-chains 78 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.0040 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN C 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3483 Z= 0.260 Angle : 0.746 11.547 4737 Z= 0.413 Chirality : 0.113 1.448 603 Planarity : 0.005 0.054 573 Dihedral : 7.725 52.161 703 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.54 % Favored : 84.46 % Rotamer: Outliers : 6.35 % Allowed : 27.51 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.95 (0.29), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.53 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.008 0.001 PHE C 237 TYR 0.014 0.002 TYR A 211 ARG 0.007 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.5995 (tmt) cc_final: 0.5569 (tmm) REVERT: B 241 GLU cc_start: 0.8104 (tt0) cc_final: 0.7810 (tt0) REVERT: A 124 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.5915 (pptt) REVERT: A 180 ARG cc_start: 0.7585 (ptp90) cc_final: 0.6527 (mmm160) REVERT: A 207 MET cc_start: 0.6128 (tmt) cc_final: 0.5720 (tmm) REVERT: A 247 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.5912 (mtp85) REVERT: C 150 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7998 (mt) REVERT: C 178 LYS cc_start: 0.7071 (ptmm) cc_final: 0.6746 (mtmm) REVERT: C 180 ARG cc_start: 0.7932 (ptp90) cc_final: 0.6817 (ptt90) REVERT: C 207 MET cc_start: 0.6655 (tmt) cc_final: 0.6228 (tmm) REVERT: C 215 THR cc_start: 0.7742 (p) cc_final: 0.7489 (t) outliers start: 24 outliers final: 10 residues processed: 106 average time/residue: 1.5059 time to fit residues: 166.6900 Evaluate side-chains 93 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3483 Z= 0.278 Angle : 0.718 11.520 4737 Z= 0.400 Chirality : 0.112 1.454 603 Planarity : 0.005 0.053 573 Dihedral : 7.606 45.224 703 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.05 % Favored : 79.95 % Rotamer: Outliers : 6.61 % Allowed : 27.78 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.80 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.42 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.007 0.002 PHE C 237 TYR 0.017 0.002 TYR C 143 ARG 0.005 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: B 168 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7797 (tm-30) REVERT: B 207 MET cc_start: 0.6219 (tmt) cc_final: 0.5697 (tmm) REVERT: B 241 GLU cc_start: 0.8206 (tt0) cc_final: 0.7938 (tt0) REVERT: A 124 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.6099 (pptt) REVERT: A 207 MET cc_start: 0.6254 (tmt) cc_final: 0.5902 (tmm) REVERT: A 233 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8296 (p) REVERT: A 247 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.5975 (mtp85) REVERT: C 128 VAL cc_start: 0.8169 (p) cc_final: 0.7807 (t) REVERT: C 150 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8195 (mt) REVERT: C 168 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: C 178 LYS cc_start: 0.7606 (ptmm) cc_final: 0.7326 (ptmt) REVERT: C 180 ARG cc_start: 0.8000 (ptp90) cc_final: 0.6847 (ptt90) REVERT: C 207 MET cc_start: 0.6845 (tmt) cc_final: 0.6464 (tmm) REVERT: C 215 THR cc_start: 0.7784 (p) cc_final: 0.7420 (t) REVERT: C 227 MET cc_start: 0.9007 (mtm) cc_final: 0.8777 (mtm) outliers start: 25 outliers final: 12 residues processed: 109 average time/residue: 1.4430 time to fit residues: 165.1271 Evaluate side-chains 103 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3483 Z= 0.355 Angle : 0.754 11.498 4737 Z= 0.423 Chirality : 0.112 1.445 603 Planarity : 0.005 0.055 573 Dihedral : 7.082 39.365 703 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.80 % Favored : 80.20 % Rotamer: Outliers : 8.73 % Allowed : 27.78 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.82 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.014 0.002 PHE C 213 TYR 0.026 0.002 TYR B 143 ARG 0.006 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: B 182 ASN cc_start: 0.8675 (t0) cc_final: 0.8418 (t0) REVERT: B 207 MET cc_start: 0.6869 (tmt) cc_final: 0.6451 (tmm) REVERT: B 241 GLU cc_start: 0.8243 (tt0) cc_final: 0.7975 (tt0) REVERT: A 124 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.6257 (pptt) REVERT: A 180 ARG cc_start: 0.7599 (ptp90) cc_final: 0.7350 (pmm-80) REVERT: A 207 MET cc_start: 0.6579 (tmt) cc_final: 0.6146 (tmm) REVERT: A 233 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8346 (p) REVERT: C 128 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7769 (t) REVERT: C 165 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7812 (pt) REVERT: C 168 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: C 178 LYS cc_start: 0.7910 (ptmm) cc_final: 0.7414 (ptmt) REVERT: C 192 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.6949 (mtt) REVERT: C 207 MET cc_start: 0.7105 (tmt) cc_final: 0.6533 (tmm) REVERT: C 215 THR cc_start: 0.7883 (p) cc_final: 0.7340 (t) outliers start: 33 outliers final: 13 residues processed: 115 average time/residue: 1.3130 time to fit residues: 158.8730 Evaluate side-chains 107 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 253 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3483 Z= 0.206 Angle : 0.658 11.316 4737 Z= 0.373 Chirality : 0.109 1.409 603 Planarity : 0.004 0.051 573 Dihedral : 6.524 42.470 703 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.55 % Favored : 81.45 % Rotamer: Outliers : 6.08 % Allowed : 30.42 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.67 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 239 PHE 0.010 0.002 PHE B 213 TYR 0.019 0.001 TYR B 143 ARG 0.006 0.001 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8341 (m) REVERT: B 161 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7739 (mt-10) REVERT: B 168 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: B 182 ASN cc_start: 0.8659 (t0) cc_final: 0.8362 (t0) REVERT: B 207 MET cc_start: 0.6896 (tmt) cc_final: 0.6405 (tmm) REVERT: B 241 GLU cc_start: 0.8189 (tt0) cc_final: 0.7898 (tt0) REVERT: A 180 ARG cc_start: 0.7418 (ptp90) cc_final: 0.7030 (pmm-80) REVERT: A 207 MET cc_start: 0.6603 (tmt) cc_final: 0.6057 (tmm) REVERT: A 247 ARG cc_start: 0.7741 (mtm-85) cc_final: 0.6011 (mtp85) REVERT: C 124 LYS cc_start: 0.8559 (mmtp) cc_final: 0.7319 (mmtt) REVERT: C 128 VAL cc_start: 0.7955 (p) cc_final: 0.7548 (t) REVERT: C 178 LYS cc_start: 0.7903 (ptmm) cc_final: 0.7462 (ptmt) REVERT: C 192 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6749 (mtt) REVERT: C 207 MET cc_start: 0.7092 (tmt) cc_final: 0.6607 (tmm) REVERT: C 215 THR cc_start: 0.7717 (p) cc_final: 0.7166 (t) REVERT: C 239 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7326 (p-80) outliers start: 23 outliers final: 10 residues processed: 106 average time/residue: 1.3485 time to fit residues: 149.9849 Evaluate side-chains 98 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN A 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.7439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3483 Z= 0.293 Angle : 0.691 11.640 4737 Z= 0.392 Chirality : 0.112 1.459 603 Planarity : 0.004 0.047 573 Dihedral : 6.511 40.544 703 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.05 % Favored : 78.95 % Rotamer: Outliers : 7.41 % Allowed : 29.10 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.69 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.33 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 239 PHE 0.006 0.001 PHE C 213 TYR 0.022 0.002 TYR C 143 ARG 0.004 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8478 (p) REVERT: B 161 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7933 (mt-10) REVERT: B 180 ARG cc_start: 0.7545 (ptp90) cc_final: 0.7257 (pmm-80) REVERT: B 182 ASN cc_start: 0.8635 (t0) cc_final: 0.8398 (t0) REVERT: B 207 MET cc_start: 0.7091 (tmt) cc_final: 0.6587 (tmm) REVERT: A 207 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6356 (tmm) REVERT: C 124 LYS cc_start: 0.8554 (mmtp) cc_final: 0.7384 (mmtt) REVERT: C 128 VAL cc_start: 0.7980 (p) cc_final: 0.7547 (t) REVERT: C 165 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7861 (pt) REVERT: C 178 LYS cc_start: 0.7937 (ptmm) cc_final: 0.7544 (ptmt) REVERT: C 192 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.6980 (mtt) REVERT: C 207 MET cc_start: 0.7153 (tmt) cc_final: 0.6679 (tmm) REVERT: C 215 THR cc_start: 0.8000 (p) cc_final: 0.7397 (t) outliers start: 28 outliers final: 17 residues processed: 109 average time/residue: 1.2865 time to fit residues: 147.2629 Evaluate side-chains 104 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.7615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3483 Z= 0.183 Angle : 0.647 11.426 4737 Z= 0.367 Chirality : 0.110 1.430 603 Planarity : 0.004 0.044 573 Dihedral : 6.109 41.031 703 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.30 % Favored : 81.70 % Rotamer: Outliers : 4.76 % Allowed : 32.80 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.56 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 239 PHE 0.007 0.001 PHE C 237 TYR 0.016 0.001 TYR C 143 ARG 0.004 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 182 ASN cc_start: 0.8618 (t0) cc_final: 0.8325 (t0) REVERT: B 207 MET cc_start: 0.7077 (tmt) cc_final: 0.6573 (tmm) REVERT: A 207 MET cc_start: 0.6729 (tmt) cc_final: 0.6273 (tmm) REVERT: A 247 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.5994 (mtp85) REVERT: C 124 LYS cc_start: 0.8500 (mmtp) cc_final: 0.7260 (mmtt) REVERT: C 128 VAL cc_start: 0.7922 (p) cc_final: 0.7491 (t) REVERT: C 155 ASN cc_start: 0.8656 (m-40) cc_final: 0.8419 (m-40) REVERT: C 163 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: C 192 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6864 (mtt) REVERT: C 207 MET cc_start: 0.7118 (tmt) cc_final: 0.6645 (tmm) REVERT: C 215 THR cc_start: 0.7605 (p) cc_final: 0.7043 (t) outliers start: 18 outliers final: 14 residues processed: 101 average time/residue: 1.4256 time to fit residues: 150.7831 Evaluate side-chains 100 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN C 148 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3483 Z= 0.197 Angle : 0.647 11.410 4737 Z= 0.367 Chirality : 0.110 1.434 603 Planarity : 0.004 0.043 573 Dihedral : 5.938 38.294 703 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.30 % Favored : 80.70 % Rotamer: Outliers : 5.29 % Allowed : 31.48 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.44 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 239 PHE 0.006 0.001 PHE C 213 TYR 0.013 0.001 TYR B 250 ARG 0.011 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 ASN cc_start: 0.8603 (t0) cc_final: 0.8308 (t0) REVERT: A 207 MET cc_start: 0.6762 (tmt) cc_final: 0.6273 (tmm) REVERT: A 247 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.6013 (mtp85) REVERT: C 124 LYS cc_start: 0.8494 (mmtp) cc_final: 0.7326 (mmtt) REVERT: C 128 VAL cc_start: 0.7919 (p) cc_final: 0.7491 (t) REVERT: C 155 ASN cc_start: 0.8619 (m-40) cc_final: 0.8383 (m-40) REVERT: C 163 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: C 168 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7138 (tm-30) REVERT: C 192 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6861 (mtt) REVERT: C 207 MET cc_start: 0.7106 (tmt) cc_final: 0.6607 (tmm) REVERT: C 215 THR cc_start: 0.7783 (p) cc_final: 0.7163 (t) outliers start: 20 outliers final: 15 residues processed: 104 average time/residue: 1.4550 time to fit residues: 158.3182 Evaluate side-chains 104 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.7814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3483 Z= 0.166 Angle : 0.638 11.368 4737 Z= 0.361 Chirality : 0.110 1.424 603 Planarity : 0.004 0.042 573 Dihedral : 5.809 37.178 703 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.05 % Favored : 81.95 % Rotamer: Outliers : 4.50 % Allowed : 33.60 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.34 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.005 0.001 PHE C 237 TYR 0.013 0.001 TYR B 211 ARG 0.013 0.001 ARG B 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.8073 (mp0) cc_final: 0.7602 (mp0) REVERT: B 182 ASN cc_start: 0.8599 (t0) cc_final: 0.8284 (t0) REVERT: A 207 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6252 (tmm) REVERT: A 247 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.6009 (mtp85) REVERT: C 124 LYS cc_start: 0.8372 (mmtp) cc_final: 0.7304 (mmtt) REVERT: C 128 VAL cc_start: 0.7888 (p) cc_final: 0.7465 (t) REVERT: C 168 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: C 192 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6767 (mtt) REVERT: C 207 MET cc_start: 0.7038 (tmt) cc_final: 0.6542 (tmm) REVERT: C 215 THR cc_start: 0.7437 (p) cc_final: 0.6862 (t) outliers start: 17 outliers final: 12 residues processed: 102 average time/residue: 1.5162 time to fit residues: 161.9871 Evaluate side-chains 104 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 GLN A 249 GLN C 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.205875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.186936 restraints weight = 11962.653| |-----------------------------------------------------------------------------| r_work (start): 0.4769 rms_B_bonded: 2.24 r_work: 0.4712 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4642 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.7928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3483 Z= 0.157 Angle : 0.629 11.370 4737 Z= 0.356 Chirality : 0.110 1.420 603 Planarity : 0.004 0.044 573 Dihedral : 5.649 34.568 703 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.05 % Favored : 81.95 % Rotamer: Outliers : 5.03 % Allowed : 33.60 % Favored : 61.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -5.23 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.006 0.001 PHE C 171 TYR 0.013 0.001 TYR A 211 ARG 0.013 0.001 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4226.85 seconds wall clock time: 75 minutes 8.52 seconds (4508.52 seconds total)