Starting phenix.real_space_refine on Tue Sep 24 03:53:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/09_2024/7u15_26278.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/09_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_26278/09_2024/7u15_26278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/09_2024/7u15_26278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/09_2024/7u15_26278.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u15_26278/09_2024/7u15_26278.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6684 Number of models: 1 Model: "" Number of chains: 2 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: "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 Restraints were copied for chains: C, B Time building chain proxies: 4.12, per 1000 atoms: 0.62 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.71 Conformation dependent library (CDL) restraints added in 434.6 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: 0.64 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: 2.10 Time building geometry restraints manager: 2.04 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: 0.00 - 5.38: 12030 5.38 - 10.76: 27 10.76 - 16.15: 3 16.15 - 21.53: 0 21.53 - 26.91: 9 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: 2811 16.15 - 32.31: 408 32.31 - 48.46: 66 48.46 - 64.61: 54 64.61 - 80.77: 15 Dihedral angle restraints: 3354 sinusoidal: 1923 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 3351 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: 485 2.19 - 2.79: 13507 2.79 - 3.40: 17853 3.40 - 4.00: 24411 4.00 - 4.60: 34874 Nonbonded interactions: 91130 Sorted by model distance: nonbonded pdb=" H VAL B 128 " pdb=" O VAL C 128 " model vdw 1.591 2.450 nonbonded pdb=" O VAL B 128 " pdb=" H VAL A 128 " model vdw 1.612 2.450 nonbonded pdb=" OG SER B 240 " pdb=" HH TYR C 236 " model vdw 1.663 2.450 nonbonded pdb=" HH TYR B 236 " pdb=" OG SER A 240 " model vdw 1.680 2.450 nonbonded pdb=" O GLU B 205 " pdb=" H GLU C 206 " model vdw 1.745 2.450 ... (remaining 91125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.030 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: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.620 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- 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= 0.395 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 : 0.522 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: 1.3627 time to fit residues: 132.8590 Evaluate side-chains 78 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 0.0870 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN B 155 ASN B 242 GLN A 154 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN C 154 ASN C 155 ASN C 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.2509 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= 0.214 Angle : 0.747 11.746 4737 Z= 0.413 Chirality : 0.112 1.528 603 Planarity : 0.005 0.049 573 Dihedral : 9.136 59.768 719 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.79 % Favored : 82.21 % Rotamer: Outliers : 6.61 % Allowed : 29.10 % Favored : 64.29 % 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: -6.17 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.70 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 239 PHE 0.013 0.002 PHE C 213 TYR 0.024 0.002 TYR B 250 ARG 0.004 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 111 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.5944 (tmt) cc_final: 0.5569 (tmm) REVERT: A 124 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.6176 (pptt) REVERT: A 140 ARG cc_start: 0.5554 (OUTLIER) cc_final: 0.2888 (tpp-160) REVERT: A 168 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7843 (tp-100) REVERT: A 178 LYS cc_start: 0.7456 (ptmm) cc_final: 0.5277 (mmmt) REVERT: A 180 ARG cc_start: 0.7481 (ptp90) cc_final: 0.6740 (mmm160) REVERT: A 207 MET cc_start: 0.5651 (tmt) cc_final: 0.5325 (tmm) REVERT: A 247 ARG cc_start: 0.7634 (mtm-85) cc_final: 0.6037 (mtp85) REVERT: C 150 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7318 (mt) REVERT: C 180 ARG cc_start: 0.7641 (ptp90) cc_final: 0.6526 (ptt90) REVERT: C 207 MET cc_start: 0.6315 (tmt) cc_final: 0.5969 (tmm) REVERT: C 227 MET cc_start: 0.8592 (mtm) cc_final: 0.8323 (mtm) outliers start: 25 outliers final: 5 residues processed: 101 average time/residue: 1.6192 time to fit residues: 170.1046 Evaluate side-chains 90 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 168 GLN 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: 3.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN A 155 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3483 Z= 0.350 Angle : 0.812 11.556 4737 Z= 0.452 Chirality : 0.115 1.470 603 Planarity : 0.005 0.060 573 Dihedral : 7.231 29.849 703 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 8.73 % Allowed : 25.13 % 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: -5.85 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 239 PHE 0.011 0.002 PHE C 171 TYR 0.017 0.002 TYR C 143 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 133 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 VAL cc_start: 0.7346 (OUTLIER) cc_final: 0.6948 (m) REVERT: B 207 MET cc_start: 0.6065 (tmt) cc_final: 0.5654 (tmm) REVERT: B 241 GLU cc_start: 0.8191 (tt0) cc_final: 0.7902 (tt0) REVERT: A 124 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.6343 (pptt) REVERT: A 163 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: A 168 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: A 180 ARG cc_start: 0.7656 (ptp90) cc_final: 0.6612 (mmm160) REVERT: A 207 MET cc_start: 0.6292 (tmt) cc_final: 0.5980 (tmm) REVERT: C 178 LYS cc_start: 0.7346 (ptmm) cc_final: 0.6951 (mtmm) REVERT: C 180 ARG cc_start: 0.7971 (ptp90) cc_final: 0.6838 (ptt90) REVERT: C 202 VAL cc_start: 0.7396 (OUTLIER) cc_final: 0.7099 (p) REVERT: C 207 MET cc_start: 0.6781 (tmt) cc_final: 0.6408 (tmm) REVERT: C 250 TYR cc_start: 0.7911 (p90) cc_final: 0.5115 (t80) outliers start: 33 outliers final: 15 residues processed: 122 average time/residue: 1.3697 time to fit residues: 174.9584 Evaluate side-chains 107 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 170 GLN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 235 THR 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 140 ARG Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 168 GLN 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 144 LEU Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 240 SER 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: 0.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.0030 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3483 Z= 0.178 Angle : 0.657 11.294 4737 Z= 0.371 Chirality : 0.110 1.414 603 Planarity : 0.004 0.042 573 Dihedral : 6.293 34.004 703 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 3.70 % Allowed : 32.01 % Favored : 64.29 % 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: -5.59 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.26 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.012 0.002 PHE A 213 TYR 0.016 0.001 TYR B 143 ARG 0.004 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 109 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.6150 (tmt) cc_final: 0.5858 (tpt) REVERT: B 241 GLU cc_start: 0.8159 (tt0) cc_final: 0.7878 (tt0) REVERT: A 180 ARG cc_start: 0.7569 (ptp90) cc_final: 0.6540 (mmm160) REVERT: A 207 MET cc_start: 0.6197 (tmt) cc_final: 0.5782 (tmt) REVERT: A 239 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7784 (p-80) REVERT: A 247 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.6201 (mtp85) REVERT: C 163 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: C 178 LYS cc_start: 0.7433 (ptmm) cc_final: 0.6751 (mtmt) REVERT: C 180 ARG cc_start: 0.7969 (ptp90) cc_final: 0.6841 (ptt90) REVERT: C 207 MET cc_start: 0.6699 (tmt) cc_final: 0.6217 (tmm) REVERT: C 250 TYR cc_start: 0.8028 (p90) cc_final: 0.5092 (t80) outliers start: 14 outliers final: 6 residues processed: 106 average time/residue: 1.3354 time to fit residues: 148.5415 Evaluate side-chains 91 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.0040 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3483 Z= 0.154 Angle : 0.626 11.316 4737 Z= 0.354 Chirality : 0.110 1.407 603 Planarity : 0.003 0.042 573 Dihedral : 5.792 33.866 703 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 3.97 % Allowed : 33.07 % Favored : 62.96 % 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: -5.48 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.007 0.001 PHE C 171 TYR 0.016 0.001 TYR B 143 ARG 0.005 0.001 ARG B 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 105 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 168 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: B 207 MET cc_start: 0.6175 (tmt) cc_final: 0.5882 (tpt) REVERT: B 239 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7491 (p-80) REVERT: B 241 GLU cc_start: 0.8139 (tt0) cc_final: 0.7855 (tt0) REVERT: A 163 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: A 180 ARG cc_start: 0.7478 (ptp90) cc_final: 0.6355 (mmm160) REVERT: A 207 MET cc_start: 0.6193 (tmt) cc_final: 0.5738 (tmt) REVERT: A 239 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.7411 (p-80) REVERT: A 247 ARG cc_start: 0.7659 (mtm-85) cc_final: 0.6146 (mtp85) REVERT: C 178 LYS cc_start: 0.7498 (ptmm) cc_final: 0.6685 (pttt) REVERT: C 180 ARG cc_start: 0.8007 (ptp90) cc_final: 0.6249 (pmt-80) REVERT: C 207 MET cc_start: 0.6777 (tmt) cc_final: 0.6364 (tmm) REVERT: C 215 THR cc_start: 0.7113 (p) cc_final: 0.6806 (t) REVERT: C 250 TYR cc_start: 0.7995 (p90) cc_final: 0.5004 (t80) outliers start: 15 outliers final: 7 residues processed: 101 average time/residue: 1.3854 time to fit residues: 146.7767 Evaluate side-chains 93 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 240 SER 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: 4.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 154 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.6138 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= 0.172 Angle : 0.627 11.406 4737 Z= 0.355 Chirality : 0.110 1.424 603 Planarity : 0.003 0.042 573 Dihedral : 5.560 31.471 703 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 4.76 % Allowed : 31.75 % 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: -5.32 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.007 0.001 PHE B 213 TYR 0.019 0.001 TYR B 143 ARG 0.002 0.000 ARG B 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 108 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: B 207 MET cc_start: 0.6240 (OUTLIER) cc_final: 0.5856 (tmm) REVERT: B 239 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7463 (p-80) REVERT: B 241 GLU cc_start: 0.8129 (tt0) cc_final: 0.7852 (tt0) REVERT: A 132 TYR cc_start: 0.8681 (t80) cc_final: 0.8161 (t80) REVERT: A 163 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: A 180 ARG cc_start: 0.7540 (ptp90) cc_final: 0.6454 (mmm160) REVERT: A 207 MET cc_start: 0.6285 (tmt) cc_final: 0.5910 (tmm) REVERT: A 239 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.7449 (p-80) REVERT: A 247 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.6132 (mtp85) REVERT: C 163 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: C 178 LYS cc_start: 0.7636 (ptmm) cc_final: 0.6818 (pttt) REVERT: C 180 ARG cc_start: 0.8035 (ptp90) cc_final: 0.6210 (pmt-80) REVERT: C 207 MET cc_start: 0.6792 (tmt) cc_final: 0.6253 (tmm) REVERT: C 215 THR cc_start: 0.7161 (p) cc_final: 0.6801 (t) REVERT: C 250 TYR cc_start: 0.8026 (p90) cc_final: 0.4976 (t80) outliers start: 18 outliers final: 10 residues processed: 101 average time/residue: 1.2915 time to fit residues: 136.9826 Evaluate side-chains 98 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 207 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 163 GLU 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: 0.0570 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 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: 5.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN A 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3483 Z= 0.217 Angle : 0.647 11.432 4737 Z= 0.366 Chirality : 0.111 1.427 603 Planarity : 0.004 0.043 573 Dihedral : 5.660 27.508 703 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.05 % Favored : 81.95 % Rotamer: Outliers : 5.82 % Allowed : 30.95 % 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: -5.35 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 239 PHE 0.004 0.001 PHE A 171 TYR 0.020 0.002 TYR B 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 109 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 140 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7523 (pmm-80) REVERT: B 207 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.6037 (tmm) REVERT: B 239 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7456 (p-80) REVERT: B 241 GLU cc_start: 0.8134 (tt0) cc_final: 0.7861 (tt0) REVERT: A 207 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.6103 (tmm) REVERT: A 239 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.7401 (p-80) REVERT: A 247 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.6176 (mtp85) REVERT: C 178 LYS cc_start: 0.7739 (ptmm) cc_final: 0.7030 (pttt) REVERT: C 207 MET cc_start: 0.6890 (tmt) cc_final: 0.6346 (tmm) REVERT: C 215 THR cc_start: 0.7446 (p) cc_final: 0.7018 (t) REVERT: C 239 HIS cc_start: 0.7228 (OUTLIER) cc_final: 0.6577 (p-80) REVERT: C 250 TYR cc_start: 0.8323 (p90) cc_final: 0.4875 (t80) outliers start: 22 outliers final: 12 residues processed: 101 average time/residue: 1.1389 time to fit residues: 121.7619 Evaluate side-chains 100 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 215 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 144 LEU Chi-restraints excluded: chain C residue 239 HIS 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: 1.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN A 148 ASN C 156 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.6858 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= 0.182 Angle : 0.630 11.387 4737 Z= 0.356 Chirality : 0.110 1.422 603 Planarity : 0.003 0.042 573 Dihedral : 5.517 27.880 703 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.79 % Favored : 82.21 % Rotamer: Outliers : 5.82 % Allowed : 30.69 % 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: -5.30 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.003 0.001 PHE B 171 TYR 0.017 0.001 TYR B 143 ARG 0.007 0.001 ARG C 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 108 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7584 (pmm-80) REVERT: B 207 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6143 (tmm) REVERT: B 239 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.7429 (p-80) REVERT: B 241 GLU cc_start: 0.8132 (tt0) cc_final: 0.7834 (tt0) REVERT: A 132 TYR cc_start: 0.8756 (t80) cc_final: 0.8454 (t80) REVERT: A 207 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6021 (tmm) REVERT: A 247 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.6158 (mtp85) REVERT: C 124 LYS cc_start: 0.8632 (mmtp) cc_final: 0.7372 (mmtt) REVERT: C 163 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: C 178 LYS cc_start: 0.7774 (ptmm) cc_final: 0.7018 (pttt) REVERT: C 207 MET cc_start: 0.6902 (tmt) cc_final: 0.6466 (tmm) REVERT: C 215 THR cc_start: 0.7434 (p) cc_final: 0.6992 (t) REVERT: C 239 HIS cc_start: 0.7154 (OUTLIER) cc_final: 0.6768 (p-80) REVERT: C 250 TYR cc_start: 0.8244 (p90) cc_final: 0.4904 (t80) outliers start: 22 outliers final: 11 residues processed: 99 average time/residue: 1.2985 time to fit residues: 135.3078 Evaluate side-chains 103 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 239 HIS 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: 4.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 242 GLN A 148 ASN A 242 GLN C 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3483 Z= 0.241 Angle : 0.663 11.491 4737 Z= 0.376 Chirality : 0.112 1.445 603 Planarity : 0.004 0.043 573 Dihedral : 5.668 27.747 703 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.05 % Favored : 81.95 % 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: -5.31 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.004 0.001 PHE B 171 TYR 0.019 0.002 TYR B 143 ARG 0.005 0.001 ARG C 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 120 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7673 (pmm-80) REVERT: B 163 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: B 207 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6389 (tmm) REVERT: B 239 HIS cc_start: 0.8049 (OUTLIER) cc_final: 0.7516 (p-80) REVERT: B 241 GLU cc_start: 0.8130 (tt0) cc_final: 0.7802 (tt0) REVERT: A 132 TYR cc_start: 0.8778 (t80) cc_final: 0.8471 (t80) REVERT: A 207 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6182 (tmm) REVERT: A 247 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.6082 (mtp85) REVERT: C 124 LYS cc_start: 0.8598 (mmtp) cc_final: 0.7350 (mmtt) REVERT: C 150 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8768 (mt) REVERT: C 178 LYS cc_start: 0.7914 (ptmm) cc_final: 0.7138 (pttt) REVERT: C 207 MET cc_start: 0.7020 (tmt) cc_final: 0.6567 (tmm) REVERT: C 250 TYR cc_start: 0.8389 (p90) cc_final: 0.4830 (t80) outliers start: 25 outliers final: 15 residues processed: 108 average time/residue: 1.2348 time to fit residues: 140.4509 Evaluate side-chains 111 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 215 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 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 239 HIS 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: 0.0670 chunk 24 optimal weight: 0.0970 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN A 148 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN C 156 ASN C 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.7391 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= 0.152 Angle : 0.615 11.357 4737 Z= 0.350 Chirality : 0.109 1.420 603 Planarity : 0.003 0.042 573 Dihedral : 5.323 28.310 703 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.04 % Favored : 84.96 % Rotamer: Outliers : 4.50 % Allowed : 32.01 % 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: -5.26 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 239 PHE 0.004 0.001 PHE C 237 TYR 0.013 0.001 TYR B 211 ARG 0.002 0.000 ARG C 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 108 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6239 (ptm-80) REVERT: B 163 GLU cc_start: 0.7765 (mp0) cc_final: 0.7558 (mp0) REVERT: B 207 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6444 (tmm) REVERT: B 241 GLU cc_start: 0.8077 (tt0) cc_final: 0.7829 (tt0) REVERT: A 132 TYR cc_start: 0.8790 (t80) cc_final: 0.8494 (t80) REVERT: A 207 MET cc_start: 0.6605 (tmt) cc_final: 0.6161 (tmm) REVERT: A 239 HIS cc_start: 0.7740 (p90) cc_final: 0.7469 (p-80) REVERT: A 247 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.6109 (mtp85) REVERT: C 124 LYS cc_start: 0.8485 (mmtp) cc_final: 0.7201 (mmtt) REVERT: C 163 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: C 178 LYS cc_start: 0.7659 (ptmm) cc_final: 0.6999 (pttt) REVERT: C 207 MET cc_start: 0.6970 (tmt) cc_final: 0.6396 (tmm) REVERT: C 215 THR cc_start: 0.7218 (p) cc_final: 0.6729 (t) REVERT: C 250 TYR cc_start: 0.8282 (p90) cc_final: 0.4838 (t80) outliers start: 17 outliers final: 10 residues processed: 103 average time/residue: 1.2795 time to fit residues: 138.5881 Evaluate side-chains 99 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 207 MET 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 208 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 163 GLU 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: 5.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN A 242 GLN C 156 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.213843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.195648 restraints weight = 11955.065| |-----------------------------------------------------------------------------| r_work (start): 0.4859 rms_B_bonded: 2.09 r_work: 0.4803 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4732 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3483 Z= 0.181 Angle : 0.627 11.443 4737 Z= 0.355 Chirality : 0.110 1.428 603 Planarity : 0.003 0.042 573 Dihedral : 5.221 26.961 703 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.79 % Favored : 83.21 % Rotamer: Outliers : 4.50 % Allowed : 32.54 % Favored : 62.96 % 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: -5.22 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 239 PHE 0.005 0.001 PHE B 171 TYR 0.013 0.001 TYR C 143 ARG 0.006 0.001 ARG C 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4003.10 seconds wall clock time: 70 minutes 19.76 seconds (4219.76 seconds total)