Starting phenix.real_space_refine on Sun Mar 10 15:01:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/03_2024/6mlu_9146.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/03_2024/6mlu_9146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/03_2024/6mlu_9146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/03_2024/6mlu_9146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/03_2024/6mlu_9146.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/03_2024/6mlu_9146.pdb" } resolution = 4.0 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= 0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 1616 2.51 5 N 426 2.21 5 O 446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1258 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1258 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Time building chain proxies: 1.87, per 1000 atoms: 0.74 Number of scatterers: 2516 At special positions: 0 Unit cell: (72.05, 73.36, 58.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 446 8.00 N 426 7.00 C 1616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 164 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 429.5 milliseconds 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 596 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 24.2% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 173 through 184 Processing helix chain 'A' and resid 184 through 190 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 173 through 184 Processing helix chain 'B' and resid 184 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 93 removed outlier: 4.585A pdb=" N VAL A 232 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 231 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU A 159 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP A 154 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 161 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ARG A 153 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU A 159 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP A 154 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 161 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 93 removed outlier: 4.583A pdb=" N VAL B 232 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 231 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU B 159 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 154 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 161 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG B 153 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU B 159 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 154 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 161 " --> pdb=" O MET B 152 " (cutoff:3.500A) 108 hydrogen bonds defined for protein. 300 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: 0.61 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 796 1.34 - 1.46: 577 1.46 - 1.58: 1159 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 2580 Sorted by residual: bond pdb=" CA HIS A 110 " pdb=" CB HIS A 110 " ideal model delta sigma weight residual 1.530 1.564 -0.033 1.69e-02 3.50e+03 3.91e+00 bond pdb=" CA HIS B 110 " pdb=" CB HIS B 110 " ideal model delta sigma weight residual 1.530 1.564 -0.033 1.69e-02 3.50e+03 3.89e+00 bond pdb=" CA ARG A 88 " pdb=" C ARG A 88 " ideal model delta sigma weight residual 1.525 1.555 -0.030 2.10e-02 2.27e+03 2.02e+00 bond pdb=" CA ARG B 88 " pdb=" C ARG B 88 " ideal model delta sigma weight residual 1.525 1.554 -0.029 2.10e-02 2.27e+03 1.88e+00 bond pdb=" N HIS B 110 " pdb=" CA HIS B 110 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.45e+00 ... (remaining 2575 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.65: 81 105.65 - 112.73: 1335 112.73 - 119.81: 849 119.81 - 126.89: 1178 126.89 - 133.97: 51 Bond angle restraints: 3494 Sorted by residual: angle pdb=" C ALA A 109 " pdb=" N HIS A 110 " pdb=" CA HIS A 110 " ideal model delta sigma weight residual 121.54 131.86 -10.32 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C ALA B 109 " pdb=" N HIS B 110 " pdb=" CA HIS B 110 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C LEU B 98 " pdb=" N GLU B 99 " pdb=" CA GLU B 99 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C LEU A 98 " pdb=" N GLU A 99 " pdb=" CA GLU A 99 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C LEU B 208 " pdb=" N GLU B 209 " pdb=" CA GLU B 209 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 ... (remaining 3489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.37: 1401 11.37 - 22.73: 135 22.73 - 34.09: 24 34.09 - 45.46: 12 45.46 - 56.82: 6 Dihedral angle restraints: 1578 sinusoidal: 664 harmonic: 914 Sorted by residual: dihedral pdb=" CA HIS B 110 " pdb=" C HIS B 110 " pdb=" N VAL B 111 " pdb=" CA VAL B 111 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA HIS A 110 " pdb=" C HIS A 110 " pdb=" N VAL A 111 " pdb=" CA VAL A 111 " ideal model delta harmonic sigma weight residual 180.00 156.82 23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA TRP A 192 " pdb=" C TRP A 192 " pdb=" N LYS A 193 " pdb=" CA LYS A 193 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 1575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 277 0.055 - 0.109: 74 0.109 - 0.164: 28 0.164 - 0.218: 7 0.218 - 0.273: 2 Chirality restraints: 388 Sorted by residual: chirality pdb=" CA HIS B 110 " pdb=" N HIS B 110 " pdb=" C HIS B 110 " pdb=" CB HIS B 110 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA HIS A 110 " pdb=" N HIS A 110 " pdb=" C HIS A 110 " pdb=" CB HIS A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB THR B 100 " pdb=" CA THR B 100 " pdb=" OG1 THR B 100 " pdb=" CG2 THR B 100 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 385 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 209 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C GLU B 209 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU B 209 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU B 210 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 209 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C GLU A 209 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU A 209 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 210 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 109 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ALA B 109 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA B 109 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS B 110 " 0.010 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 921 2.90 - 3.40: 2472 3.40 - 3.90: 4091 3.90 - 4.40: 4488 4.40 - 4.90: 7629 Nonbonded interactions: 19601 Sorted by model distance: nonbonded pdb=" OD1 ASP A 154 " pdb=" N MET A 158 " model vdw 2.406 2.520 nonbonded pdb=" OD1 ASP B 154 " pdb=" N MET B 158 " model vdw 2.409 2.520 nonbonded pdb=" NH1 ARG B 206 " pdb=" O PHE B 240 " model vdw 2.415 2.520 nonbonded pdb=" NH1 ARG A 206 " pdb=" O PHE A 240 " model vdw 2.415 2.520 nonbonded pdb=" OH TYR A 230 " pdb=" N TYR B 171 " model vdw 2.432 2.520 ... (remaining 19596 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.540 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.690 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.005 0.044 2580 Z= 0.345 Angle : 1.046 10.429 3494 Z= 0.564 Chirality : 0.064 0.273 388 Planarity : 0.007 0.036 440 Dihedral : 9.856 47.411 976 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 0.69 % Allowed : 2.78 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.42), residues: 302 helix: -2.79 (0.45), residues: 74 sheet: -1.76 (0.57), residues: 86 loop : -3.75 (0.42), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 192 HIS 0.013 0.004 HIS A 110 PHE 0.015 0.003 PHE A 196 TYR 0.008 0.002 TYR B 155 ARG 0.002 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8839 (m-30) cc_final: 0.8375 (m-30) REVERT: A 137 SER cc_start: 0.9203 (t) cc_final: 0.8998 (p) REVERT: A 147 MET cc_start: 0.8306 (mmm) cc_final: 0.7641 (tpp) REVERT: A 165 ARG cc_start: 0.7552 (mmt-90) cc_final: 0.7122 (mmt180) REVERT: A 177 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7831 (mtm-85) REVERT: A 195 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7635 (mt-10) REVERT: A 197 GLN cc_start: 0.8825 (mt0) cc_final: 0.8597 (mp-120) REVERT: A 198 GLN cc_start: 0.8748 (mt0) cc_final: 0.8529 (mt0) REVERT: A 202 GLU cc_start: 0.8764 (tt0) cc_final: 0.8201 (tm-30) REVERT: A 204 PHE cc_start: 0.8056 (m-80) cc_final: 0.7746 (m-80) REVERT: A 223 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8401 (mm-40) REVERT: A 232 VAL cc_start: 0.9659 (t) cc_final: 0.8480 (t) REVERT: A 236 ILE cc_start: 0.9238 (mt) cc_final: 0.8963 (tp) REVERT: A 237 VAL cc_start: 0.8740 (m) cc_final: 0.8274 (p) REVERT: A 239 ASP cc_start: 0.8777 (m-30) cc_final: 0.8247 (m-30) REVERT: B 115 LYS cc_start: 0.6956 (ttmp) cc_final: 0.6727 (tptm) REVERT: B 133 ASP cc_start: 0.8724 (m-30) cc_final: 0.8410 (m-30) REVERT: B 177 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.8038 (mtm-85) REVERT: B 202 GLU cc_start: 0.8888 (tt0) cc_final: 0.8301 (tm-30) REVERT: B 232 VAL cc_start: 0.9717 (t) cc_final: 0.8700 (t) REVERT: B 236 ILE cc_start: 0.9343 (mt) cc_final: 0.9043 (tp) REVERT: B 237 VAL cc_start: 0.8879 (m) cc_final: 0.8238 (p) REVERT: B 239 ASP cc_start: 0.8877 (m-30) cc_final: 0.8536 (p0) outliers start: 2 outliers final: 0 residues processed: 163 average time/residue: 0.2183 time to fit residues: 39.2854 Evaluate side-chains 124 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 0.0000 chunk 8 optimal weight: 5.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2580 Z= 0.220 Angle : 0.782 7.074 3494 Z= 0.411 Chirality : 0.053 0.186 388 Planarity : 0.005 0.030 440 Dihedral : 6.185 23.144 336 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 7.64 % Allowed : 17.01 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.46), residues: 302 helix: -0.62 (0.58), residues: 74 sheet: -1.69 (0.54), residues: 90 loop : -3.50 (0.47), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 192 HIS 0.010 0.002 HIS B 110 PHE 0.015 0.002 PHE B 106 TYR 0.007 0.001 TYR A 219 ARG 0.004 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8743 (pm20) cc_final: 0.8441 (pm20) REVERT: A 120 LEU cc_start: 0.8698 (mt) cc_final: 0.8357 (mt) REVERT: A 124 GLN cc_start: 0.7190 (mp10) cc_final: 0.5856 (tm-30) REVERT: A 133 ASP cc_start: 0.8748 (m-30) cc_final: 0.8207 (m-30) REVERT: A 145 MET cc_start: 0.8483 (ttm) cc_final: 0.7840 (mtt) REVERT: A 147 MET cc_start: 0.8138 (mmm) cc_final: 0.7458 (tpp) REVERT: A 165 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7257 (mmt180) REVERT: A 198 GLN cc_start: 0.8624 (mt0) cc_final: 0.8283 (mt0) REVERT: A 202 GLU cc_start: 0.8593 (tt0) cc_final: 0.8014 (tm-30) REVERT: A 204 PHE cc_start: 0.8085 (m-80) cc_final: 0.7597 (m-80) REVERT: A 236 ILE cc_start: 0.9276 (mt) cc_final: 0.9034 (tp) REVERT: A 237 VAL cc_start: 0.9092 (m) cc_final: 0.8586 (p) REVERT: A 239 ASP cc_start: 0.8812 (m-30) cc_final: 0.8343 (m-30) REVERT: B 115 LYS cc_start: 0.6919 (ttmp) cc_final: 0.6566 (tptm) REVERT: B 120 LEU cc_start: 0.8819 (mt) cc_final: 0.8410 (mm) REVERT: B 124 GLN cc_start: 0.7975 (mp10) cc_final: 0.7630 (tm-30) REVERT: B 127 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8141 (ptmt) REVERT: B 152 MET cc_start: 0.7620 (mmm) cc_final: 0.7203 (mmm) REVERT: B 202 GLU cc_start: 0.8866 (tt0) cc_final: 0.8454 (tm-30) REVERT: B 204 PHE cc_start: 0.8038 (m-80) cc_final: 0.7712 (m-10) REVERT: B 211 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.7987 (mmp80) REVERT: B 223 GLN cc_start: 0.8470 (mm110) cc_final: 0.7873 (mm-40) REVERT: B 225 GLN cc_start: 0.8946 (pm20) cc_final: 0.8671 (pm20) REVERT: B 226 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8880 (mmmt) REVERT: B 236 ILE cc_start: 0.9345 (mt) cc_final: 0.8978 (tp) REVERT: B 237 VAL cc_start: 0.9091 (m) cc_final: 0.8247 (p) REVERT: B 239 ASP cc_start: 0.8977 (m-30) cc_final: 0.8161 (p0) outliers start: 22 outliers final: 10 residues processed: 136 average time/residue: 0.1995 time to fit residues: 30.2930 Evaluate side-chains 131 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 227 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2580 Z= 0.252 Angle : 0.754 7.334 3494 Z= 0.395 Chirality : 0.052 0.205 388 Planarity : 0.005 0.026 440 Dihedral : 6.123 21.873 336 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 24.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 9.72 % Allowed : 20.49 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.46), residues: 302 helix: 0.17 (0.58), residues: 74 sheet: -1.99 (0.51), residues: 94 loop : -3.18 (0.50), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 192 HIS 0.012 0.003 HIS B 110 PHE 0.018 0.002 PHE B 106 TYR 0.022 0.002 TYR A 126 ARG 0.004 0.000 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7823 (tptm) cc_final: 0.7426 (mttm) REVERT: A 119 LEU cc_start: 0.7813 (mt) cc_final: 0.7549 (mt) REVERT: A 120 LEU cc_start: 0.8645 (mt) cc_final: 0.8219 (mt) REVERT: A 124 GLN cc_start: 0.7927 (mp10) cc_final: 0.7200 (tm-30) REVERT: A 133 ASP cc_start: 0.8827 (m-30) cc_final: 0.8170 (m-30) REVERT: A 136 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8372 (mp0) REVERT: A 139 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7877 (tp-100) REVERT: A 152 MET cc_start: 0.7287 (mmm) cc_final: 0.6940 (mmm) REVERT: A 198 GLN cc_start: 0.8582 (mt0) cc_final: 0.8098 (mt0) REVERT: A 202 GLU cc_start: 0.8574 (tt0) cc_final: 0.8346 (tm-30) REVERT: A 204 PHE cc_start: 0.8072 (m-80) cc_final: 0.7679 (m-80) REVERT: A 223 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8287 (mm-40) REVERT: A 236 ILE cc_start: 0.9377 (mt) cc_final: 0.9033 (tp) REVERT: A 237 VAL cc_start: 0.9099 (m) cc_final: 0.8567 (p) REVERT: A 239 ASP cc_start: 0.8744 (m-30) cc_final: 0.8279 (m-30) REVERT: B 115 LYS cc_start: 0.7119 (ttmp) cc_final: 0.6639 (tptp) REVERT: B 120 LEU cc_start: 0.8806 (mt) cc_final: 0.8578 (mm) REVERT: B 121 MET cc_start: 0.6730 (tmm) cc_final: 0.6422 (tpp) REVERT: B 124 GLN cc_start: 0.8448 (mp10) cc_final: 0.8148 (tm-30) REVERT: B 126 TYR cc_start: 0.6915 (m-80) cc_final: 0.6567 (m-80) REVERT: B 136 GLU cc_start: 0.8617 (mp0) cc_final: 0.8304 (mp0) REVERT: B 152 MET cc_start: 0.7790 (mmm) cc_final: 0.7292 (mmm) REVERT: B 202 GLU cc_start: 0.8772 (tt0) cc_final: 0.8387 (tm-30) REVERT: B 204 PHE cc_start: 0.8313 (m-80) cc_final: 0.7764 (m-10) REVERT: B 211 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.7880 (mmp80) REVERT: B 218 VAL cc_start: 0.9418 (m) cc_final: 0.9130 (t) REVERT: B 236 ILE cc_start: 0.9330 (mt) cc_final: 0.8981 (tp) REVERT: B 237 VAL cc_start: 0.9133 (m) cc_final: 0.8655 (p) REVERT: B 239 ASP cc_start: 0.8985 (m-30) cc_final: 0.8468 (m-30) outliers start: 28 outliers final: 21 residues processed: 132 average time/residue: 0.1860 time to fit residues: 27.6460 Evaluate side-chains 136 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 40.0000 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2580 Z= 0.220 Angle : 0.729 6.582 3494 Z= 0.379 Chirality : 0.051 0.199 388 Planarity : 0.004 0.031 440 Dihedral : 6.015 22.907 336 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 8.68 % Allowed : 21.88 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.47), residues: 302 helix: 0.67 (0.58), residues: 74 sheet: -2.00 (0.51), residues: 94 loop : -3.12 (0.50), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 192 HIS 0.011 0.003 HIS A 110 PHE 0.018 0.001 PHE B 106 TYR 0.037 0.002 TYR A 126 ARG 0.003 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8860 (pp30) cc_final: 0.8472 (pm20) REVERT: A 115 LYS cc_start: 0.7560 (tptm) cc_final: 0.7294 (mttm) REVERT: A 120 LEU cc_start: 0.8668 (mt) cc_final: 0.8234 (mt) REVERT: A 124 GLN cc_start: 0.7834 (mp10) cc_final: 0.7209 (tm-30) REVERT: A 126 TYR cc_start: 0.6529 (m-80) cc_final: 0.6168 (m-80) REVERT: A 133 ASP cc_start: 0.8776 (m-30) cc_final: 0.8081 (m-30) REVERT: A 134 MET cc_start: 0.8969 (ptp) cc_final: 0.8717 (mtm) REVERT: A 136 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8340 (mp0) REVERT: A 139 GLN cc_start: 0.8290 (tp-100) cc_final: 0.7843 (tp-100) REVERT: A 152 MET cc_start: 0.7229 (mmm) cc_final: 0.6863 (mmm) REVERT: A 195 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7162 (mt-10) REVERT: A 198 GLN cc_start: 0.8581 (mt0) cc_final: 0.7940 (mt0) REVERT: A 202 GLU cc_start: 0.8626 (tt0) cc_final: 0.8096 (tm-30) REVERT: A 204 PHE cc_start: 0.7768 (m-80) cc_final: 0.7492 (m-80) REVERT: A 223 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8212 (mm-40) REVERT: A 236 ILE cc_start: 0.9311 (mt) cc_final: 0.8785 (tp) REVERT: A 237 VAL cc_start: 0.9097 (m) cc_final: 0.8611 (p) REVERT: A 239 ASP cc_start: 0.8709 (m-30) cc_final: 0.8122 (m-30) REVERT: B 115 LYS cc_start: 0.7450 (ttmp) cc_final: 0.6742 (tptm) REVERT: B 116 LYS cc_start: 0.7280 (pmtt) cc_final: 0.6741 (ptmt) REVERT: B 120 LEU cc_start: 0.8832 (mt) cc_final: 0.8616 (mm) REVERT: B 121 MET cc_start: 0.6694 (tmm) cc_final: 0.6381 (tpp) REVERT: B 124 GLN cc_start: 0.8458 (mp10) cc_final: 0.8112 (tm-30) REVERT: B 126 TYR cc_start: 0.6649 (m-80) cc_final: 0.6337 (m-80) REVERT: B 136 GLU cc_start: 0.8705 (mp0) cc_final: 0.8364 (mp0) REVERT: B 152 MET cc_start: 0.7760 (mmm) cc_final: 0.7502 (mmm) REVERT: B 184 LEU cc_start: 0.8925 (mm) cc_final: 0.8679 (mm) REVERT: B 195 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7081 (tt0) REVERT: B 202 GLU cc_start: 0.8748 (tt0) cc_final: 0.8513 (tm-30) REVERT: B 204 PHE cc_start: 0.8359 (m-80) cc_final: 0.7758 (m-10) REVERT: B 236 ILE cc_start: 0.9284 (mt) cc_final: 0.8961 (tp) REVERT: B 237 VAL cc_start: 0.9106 (m) cc_final: 0.8620 (p) REVERT: B 239 ASP cc_start: 0.8950 (m-30) cc_final: 0.8482 (m-30) outliers start: 25 outliers final: 17 residues processed: 127 average time/residue: 0.1873 time to fit residues: 26.8130 Evaluate side-chains 132 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2580 Z= 0.319 Angle : 0.778 7.071 3494 Z= 0.406 Chirality : 0.052 0.207 388 Planarity : 0.005 0.028 440 Dihedral : 6.247 23.280 336 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 29.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 10.07 % Allowed : 23.61 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.47), residues: 302 helix: 1.02 (0.61), residues: 74 sheet: -2.10 (0.50), residues: 94 loop : -3.06 (0.49), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 182 HIS 0.012 0.004 HIS A 110 PHE 0.019 0.002 PHE B 106 TYR 0.027 0.002 TYR A 126 ARG 0.004 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7850 (tptm) cc_final: 0.7517 (mttm) REVERT: A 120 LEU cc_start: 0.8752 (mt) cc_final: 0.8282 (mt) REVERT: A 124 GLN cc_start: 0.7791 (mp10) cc_final: 0.7071 (tm-30) REVERT: A 139 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8405 (tp-100) REVERT: A 152 MET cc_start: 0.7531 (mmm) cc_final: 0.7235 (mmm) REVERT: A 198 GLN cc_start: 0.8525 (mt0) cc_final: 0.7639 (pp30) REVERT: A 204 PHE cc_start: 0.7973 (m-80) cc_final: 0.7510 (m-80) REVERT: A 236 ILE cc_start: 0.9372 (mt) cc_final: 0.8755 (tp) REVERT: A 237 VAL cc_start: 0.9031 (m) cc_final: 0.8527 (p) REVERT: A 239 ASP cc_start: 0.8702 (m-30) cc_final: 0.8172 (m-30) REVERT: B 115 LYS cc_start: 0.7563 (ttmp) cc_final: 0.6885 (tptp) REVERT: B 120 LEU cc_start: 0.8721 (mt) cc_final: 0.8414 (mt) REVERT: B 121 MET cc_start: 0.6691 (tmm) cc_final: 0.6364 (tpp) REVERT: B 124 GLN cc_start: 0.8487 (mp10) cc_final: 0.8036 (tm-30) REVERT: B 126 TYR cc_start: 0.6643 (m-80) cc_final: 0.6279 (m-80) REVERT: B 136 GLU cc_start: 0.8766 (mp0) cc_final: 0.8466 (mp0) REVERT: B 202 GLU cc_start: 0.8750 (tt0) cc_final: 0.8507 (tm-30) REVERT: B 236 ILE cc_start: 0.9302 (mt) cc_final: 0.8957 (tp) REVERT: B 237 VAL cc_start: 0.9118 (m) cc_final: 0.8611 (p) REVERT: B 239 ASP cc_start: 0.9024 (m-30) cc_final: 0.8602 (m-30) outliers start: 29 outliers final: 16 residues processed: 126 average time/residue: 0.1841 time to fit residues: 26.2012 Evaluate side-chains 125 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2580 Z= 0.250 Angle : 0.808 6.487 3494 Z= 0.413 Chirality : 0.054 0.199 388 Planarity : 0.005 0.034 440 Dihedral : 6.282 23.670 336 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 25.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 8.68 % Allowed : 25.35 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.48), residues: 302 helix: 0.93 (0.61), residues: 74 sheet: -1.79 (0.53), residues: 90 loop : -3.17 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.011 0.003 HIS A 110 PHE 0.018 0.002 PHE B 106 TYR 0.038 0.002 TYR A 126 ARG 0.003 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9012 (pp30) cc_final: 0.8359 (pm20) REVERT: A 115 LYS cc_start: 0.7696 (tptm) cc_final: 0.7391 (mttm) REVERT: A 133 ASP cc_start: 0.8909 (m-30) cc_final: 0.8317 (m-30) REVERT: A 136 GLU cc_start: 0.8713 (mp0) cc_final: 0.8355 (mp0) REVERT: A 139 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8068 (tp-100) REVERT: A 152 MET cc_start: 0.7210 (mmm) cc_final: 0.6992 (mmm) REVERT: A 198 GLN cc_start: 0.8432 (mt0) cc_final: 0.8200 (mt0) REVERT: A 221 GLU cc_start: 0.7943 (pp20) cc_final: 0.7090 (pp20) REVERT: A 223 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8314 (mm-40) REVERT: A 236 ILE cc_start: 0.9347 (mt) cc_final: 0.8695 (tp) REVERT: A 237 VAL cc_start: 0.8929 (m) cc_final: 0.8419 (p) REVERT: A 239 ASP cc_start: 0.8691 (m-30) cc_final: 0.8253 (m-30) REVERT: B 91 HIS cc_start: 0.7182 (OUTLIER) cc_final: 0.6905 (m-70) REVERT: B 120 LEU cc_start: 0.8792 (mt) cc_final: 0.8528 (mm) REVERT: B 121 MET cc_start: 0.6667 (tmm) cc_final: 0.6347 (tpp) REVERT: B 124 GLN cc_start: 0.8474 (mp10) cc_final: 0.8061 (tm-30) REVERT: B 126 TYR cc_start: 0.6475 (m-10) cc_final: 0.6178 (m-80) REVERT: B 136 GLU cc_start: 0.8798 (mp0) cc_final: 0.8502 (mp0) REVERT: B 195 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7470 (tt0) REVERT: B 202 GLU cc_start: 0.8721 (tt0) cc_final: 0.8509 (tm-30) REVERT: B 221 GLU cc_start: 0.8364 (pt0) cc_final: 0.7989 (tm-30) REVERT: B 236 ILE cc_start: 0.9280 (mt) cc_final: 0.8937 (tp) REVERT: B 237 VAL cc_start: 0.9095 (m) cc_final: 0.8553 (p) REVERT: B 239 ASP cc_start: 0.8983 (m-30) cc_final: 0.8498 (m-30) outliers start: 25 outliers final: 19 residues processed: 125 average time/residue: 0.1841 time to fit residues: 25.9206 Evaluate side-chains 131 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2580 Z= 0.225 Angle : 0.795 9.597 3494 Z= 0.399 Chirality : 0.052 0.194 388 Planarity : 0.005 0.036 440 Dihedral : 6.163 23.275 336 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 9.38 % Allowed : 26.04 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.49), residues: 302 helix: 0.99 (0.63), residues: 72 sheet: -1.59 (0.55), residues: 90 loop : -3.15 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 192 HIS 0.011 0.003 HIS A 110 PHE 0.017 0.001 PHE B 106 TYR 0.029 0.002 TYR A 126 ARG 0.003 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7690 (tptm) cc_final: 0.7258 (mttm) REVERT: A 133 ASP cc_start: 0.8801 (m-30) cc_final: 0.8214 (m-30) REVERT: A 136 GLU cc_start: 0.8736 (mp0) cc_final: 0.8308 (mp0) REVERT: A 139 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8021 (tp-100) REVERT: A 195 GLU cc_start: 0.7933 (mt-10) cc_final: 0.6948 (tt0) REVERT: A 221 GLU cc_start: 0.7819 (pp20) cc_final: 0.6947 (pp20) REVERT: A 223 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8444 (mm-40) REVERT: A 236 ILE cc_start: 0.9258 (mt) cc_final: 0.8767 (tp) REVERT: A 237 VAL cc_start: 0.8837 (m) cc_final: 0.7997 (p) REVERT: A 239 ASP cc_start: 0.8544 (m-30) cc_final: 0.7959 (m-30) REVERT: B 91 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6981 (m-70) REVERT: B 120 LEU cc_start: 0.8821 (mt) cc_final: 0.8583 (mm) REVERT: B 121 MET cc_start: 0.6675 (tmm) cc_final: 0.6437 (tpp) REVERT: B 124 GLN cc_start: 0.8441 (mp10) cc_final: 0.8073 (tm-30) REVERT: B 135 PRO cc_start: 0.9482 (Cg_endo) cc_final: 0.9181 (Cg_exo) REVERT: B 136 GLU cc_start: 0.8687 (mp0) cc_final: 0.8406 (mp0) REVERT: B 152 MET cc_start: 0.7769 (mmm) cc_final: 0.7428 (mmm) REVERT: B 195 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7494 (tt0) REVERT: B 198 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7680 (pp30) REVERT: B 204 PHE cc_start: 0.8449 (m-80) cc_final: 0.7805 (m-10) REVERT: B 211 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7974 (mtp85) REVERT: B 212 GLN cc_start: 0.8665 (mp10) cc_final: 0.8223 (mp10) REVERT: B 221 GLU cc_start: 0.8386 (pt0) cc_final: 0.7995 (tm-30) REVERT: B 236 ILE cc_start: 0.9179 (mt) cc_final: 0.8898 (tp) REVERT: B 237 VAL cc_start: 0.9085 (m) cc_final: 0.8535 (p) REVERT: B 239 ASP cc_start: 0.8971 (m-30) cc_final: 0.8485 (m-30) outliers start: 27 outliers final: 19 residues processed: 132 average time/residue: 0.1879 time to fit residues: 27.8947 Evaluate side-chains 136 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 2580 Z= 0.354 Angle : 0.913 12.342 3494 Z= 0.460 Chirality : 0.055 0.208 388 Planarity : 0.006 0.042 440 Dihedral : 6.528 23.497 336 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 33.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.91 % Favored : 87.09 % Rotamer: Outliers : 11.11 % Allowed : 26.39 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.49), residues: 302 helix: 0.81 (0.64), residues: 74 sheet: -1.87 (0.54), residues: 90 loop : -3.05 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 192 HIS 0.012 0.003 HIS A 110 PHE 0.022 0.002 PHE B 106 TYR 0.036 0.003 TYR B 126 ARG 0.003 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7854 (tptm) cc_final: 0.7327 (mttm) REVERT: A 136 GLU cc_start: 0.8732 (mp0) cc_final: 0.8181 (mp0) REVERT: A 139 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8460 (tp-100) REVERT: A 236 ILE cc_start: 0.9386 (mt) cc_final: 0.8780 (tp) REVERT: A 237 VAL cc_start: 0.8913 (m) cc_final: 0.8331 (p) REVERT: A 239 ASP cc_start: 0.8550 (m-30) cc_final: 0.8055 (m-30) REVERT: B 120 LEU cc_start: 0.8668 (mt) cc_final: 0.8442 (mm) REVERT: B 124 GLN cc_start: 0.8361 (mp10) cc_final: 0.8055 (tm-30) REVERT: B 126 TYR cc_start: 0.6185 (m-80) cc_final: 0.5296 (m-80) REVERT: B 136 GLU cc_start: 0.8714 (mp0) cc_final: 0.8493 (mp0) REVERT: B 152 MET cc_start: 0.8004 (mmm) cc_final: 0.7769 (mmm) REVERT: B 195 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6936 (tt0) REVERT: B 221 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: B 237 VAL cc_start: 0.9083 (m) cc_final: 0.8545 (p) REVERT: B 239 ASP cc_start: 0.8951 (m-30) cc_final: 0.8494 (m-30) outliers start: 32 outliers final: 28 residues processed: 121 average time/residue: 0.1687 time to fit residues: 23.2614 Evaluate side-chains 131 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.6910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 2580 Z= 0.264 Angle : 0.907 12.270 3494 Z= 0.443 Chirality : 0.055 0.198 388 Planarity : 0.005 0.045 440 Dihedral : 6.349 23.039 336 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 29.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 9.03 % Allowed : 29.86 % Favored : 61.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.49), residues: 302 helix: 0.62 (0.65), residues: 74 sheet: -1.80 (0.54), residues: 90 loop : -3.07 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 192 HIS 0.011 0.002 HIS A 110 PHE 0.020 0.002 PHE B 106 TYR 0.030 0.002 TYR A 126 ARG 0.004 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7610 (tptm) cc_final: 0.7197 (mttm) REVERT: A 136 GLU cc_start: 0.8737 (mp0) cc_final: 0.8185 (mp0) REVERT: A 139 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8351 (tp-100) REVERT: A 152 MET cc_start: 0.7054 (mmm) cc_final: 0.6789 (mmm) REVERT: A 223 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8515 (mm-40) REVERT: A 236 ILE cc_start: 0.9336 (mt) cc_final: 0.8816 (tp) REVERT: A 237 VAL cc_start: 0.8877 (m) cc_final: 0.7975 (p) REVERT: A 239 ASP cc_start: 0.8626 (m-30) cc_final: 0.8088 (m-30) REVERT: A 240 PHE cc_start: 0.5311 (p90) cc_final: 0.4085 (m-80) REVERT: B 91 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6694 (m-70) REVERT: B 120 LEU cc_start: 0.8671 (mt) cc_final: 0.8460 (mm) REVERT: B 124 GLN cc_start: 0.8380 (mp10) cc_final: 0.8010 (tm-30) REVERT: B 126 TYR cc_start: 0.6148 (m-80) cc_final: 0.4910 (m-80) REVERT: B 135 PRO cc_start: 0.9414 (Cg_endo) cc_final: 0.9132 (Cg_exo) REVERT: B 136 GLU cc_start: 0.8668 (mp0) cc_final: 0.8401 (mp0) REVERT: B 152 MET cc_start: 0.8068 (mmm) cc_final: 0.7811 (mmm) REVERT: B 170 ARG cc_start: 0.9106 (tpp-160) cc_final: 0.7987 (mmt-90) REVERT: B 195 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7518 (tt0) REVERT: B 211 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7893 (mmm-85) REVERT: B 221 GLU cc_start: 0.8354 (pt0) cc_final: 0.8143 (tm-30) REVERT: B 236 ILE cc_start: 0.9356 (mt) cc_final: 0.8990 (tp) REVERT: B 237 VAL cc_start: 0.9062 (m) cc_final: 0.8366 (p) REVERT: B 239 ASP cc_start: 0.8977 (m-30) cc_final: 0.8457 (m-30) outliers start: 26 outliers final: 21 residues processed: 124 average time/residue: 0.1868 time to fit residues: 26.1884 Evaluate side-chains 133 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS B 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.7143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2580 Z= 0.248 Angle : 0.938 13.472 3494 Z= 0.447 Chirality : 0.055 0.190 388 Planarity : 0.005 0.042 440 Dihedral : 6.194 22.670 336 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 26.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 6.94 % Allowed : 31.25 % Favored : 61.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.49), residues: 302 helix: 0.91 (0.65), residues: 72 sheet: -1.92 (0.53), residues: 86 loop : -3.10 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 192 HIS 0.011 0.002 HIS B 110 PHE 0.017 0.001 PHE B 106 TYR 0.027 0.002 TYR A 126 ARG 0.007 0.001 ARG B 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7644 (tptm) cc_final: 0.7248 (mttm) REVERT: A 136 GLU cc_start: 0.8625 (mp0) cc_final: 0.7923 (mp0) REVERT: A 139 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8114 (tp-100) REVERT: A 193 LYS cc_start: 0.7470 (mmtm) cc_final: 0.6995 (mmtp) REVERT: A 223 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8514 (mm-40) REVERT: A 236 ILE cc_start: 0.9280 (mt) cc_final: 0.8750 (tp) REVERT: A 237 VAL cc_start: 0.8846 (m) cc_final: 0.7962 (p) REVERT: A 239 ASP cc_start: 0.8310 (m-30) cc_final: 0.7787 (m-30) REVERT: A 240 PHE cc_start: 0.5395 (p90) cc_final: 0.4167 (m-80) REVERT: B 124 GLN cc_start: 0.8327 (mp10) cc_final: 0.8039 (tm-30) REVERT: B 126 TYR cc_start: 0.6377 (m-80) cc_final: 0.5227 (m-80) REVERT: B 135 PRO cc_start: 0.9341 (Cg_endo) cc_final: 0.9030 (Cg_exo) REVERT: B 136 GLU cc_start: 0.8741 (mp0) cc_final: 0.8423 (mp0) REVERT: B 152 MET cc_start: 0.7935 (mmm) cc_final: 0.7507 (mmm) REVERT: B 198 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7712 (pp30) REVERT: B 204 PHE cc_start: 0.7918 (m-80) cc_final: 0.7693 (m-10) REVERT: B 211 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7930 (mmm-85) REVERT: B 222 ILE cc_start: 0.9724 (mt) cc_final: 0.9257 (mm) REVERT: B 236 ILE cc_start: 0.9314 (mt) cc_final: 0.8929 (tp) REVERT: B 237 VAL cc_start: 0.8961 (m) cc_final: 0.8253 (p) REVERT: B 239 ASP cc_start: 0.9022 (m-30) cc_final: 0.8554 (m-30) outliers start: 20 outliers final: 18 residues processed: 131 average time/residue: 0.1909 time to fit residues: 28.3443 Evaluate side-chains 133 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 234 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.109737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.088942 restraints weight = 7299.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091544 restraints weight = 4148.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093223 restraints weight = 2894.483| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 2580 Z= 0.310 Angle : 0.956 13.449 3494 Z= 0.465 Chirality : 0.055 0.188 388 Planarity : 0.006 0.047 440 Dihedral : 6.456 23.179 336 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 30.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 7.29 % Allowed : 30.90 % Favored : 61.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.49), residues: 302 helix: 0.75 (0.65), residues: 72 sheet: -1.72 (0.55), residues: 82 loop : -3.08 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.012 0.003 HIS B 110 PHE 0.016 0.002 PHE B 106 TYR 0.029 0.002 TYR A 126 ARG 0.005 0.001 ARG B 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1032.08 seconds wall clock time: 19 minutes 9.82 seconds (1149.82 seconds total)