Starting phenix.real_space_refine on Thu Sep 26 14:44:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/09_2024/7p13_13154.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/09_2024/7p13_13154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/09_2024/7p13_13154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/09_2024/7p13_13154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/09_2024/7p13_13154.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p13_13154/09_2024/7p13_13154.cif" } resolution = 2.29 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= 0.268 sd= 0.983 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 49 5.16 5 C 8463 2.51 5 N 2408 2.21 5 O 2653 1.98 5 H 154 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13727 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 4.92, per 1000 atoms: 0.36 Number of scatterers: 13727 At special positions: 0 Unit cell: (115.092, 113.424, 102.582, 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 49 16.00 O 2653 8.00 N 2408 7.00 C 8463 6.00 H 154 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 79 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 179 through 223 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 242 through 268 Proline residue: A 248 - end of helix Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 79 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 146 through 166 Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 179 through 223 Processing helix chain 'B' and resid 225 through 235 Processing helix chain 'B' and resid 242 through 268 Proline residue: B 248 - end of helix Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 79 Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 146 through 166 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 179 through 223 Processing helix chain 'C' and resid 225 through 235 Processing helix chain 'C' and resid 242 through 268 Proline residue: C 248 - end of helix Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 79 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 146 through 166 Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 179 through 223 Processing helix chain 'D' and resid 225 through 235 Processing helix chain 'D' and resid 242 through 268 Proline residue: D 248 - end of helix Processing helix chain 'E' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 79 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 146 through 166 Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 179 through 223 Processing helix chain 'E' and resid 225 through 235 Processing helix chain 'E' and resid 242 through 268 Proline residue: E 248 - end of helix Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 79 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 130 through 142 Processing helix chain 'F' and resid 146 through 166 Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 179 through 223 Processing helix chain 'F' and resid 225 through 235 Processing helix chain 'F' and resid 242 through 268 Proline residue: F 248 - end of helix Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 79 Processing helix chain 'G' and resid 80 through 82 No H-bonds generated for 'chain 'G' and resid 80 through 82' Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 146 through 166 Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 179 through 223 Processing helix chain 'G' and resid 225 through 235 Processing helix chain 'G' and resid 242 through 268 Proline residue: G 248 - end of helix 987 hydrogen bonds defined for protein. 2919 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: 3.58 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 154 1.02 - 1.21: 49 1.21 - 1.41: 5677 1.41 - 1.60: 8043 1.60 - 1.80: 84 Bond restraints: 14007 Sorted by residual: bond pdb=" C LEU G 270 " pdb=" N GLU G 271 " ideal model delta sigma weight residual 1.329 1.272 0.056 1.60e-02 3.91e+03 1.24e+01 bond pdb=" C LEU E 270 " pdb=" N GLU E 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.23e+01 bond pdb=" C LEU F 270 " pdb=" N GLU F 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.22e+01 bond pdb=" C LEU C 270 " pdb=" N GLU C 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.21e+01 bond pdb=" C LEU B 270 " pdb=" N GLU B 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.21e+01 ... (remaining 14002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 18243 2.26 - 4.53: 818 4.53 - 6.79: 112 6.79 - 9.05: 14 9.05 - 11.31: 14 Bond angle restraints: 19201 Sorted by residual: angle pdb=" C GLU D 258 " pdb=" N LYS D 259 " pdb=" CA LYS D 259 " ideal model delta sigma weight residual 121.14 115.49 5.65 1.75e+00 3.27e-01 1.04e+01 angle pdb=" C GLU E 258 " pdb=" N LYS E 259 " pdb=" CA LYS E 259 " ideal model delta sigma weight residual 121.14 115.50 5.64 1.75e+00 3.27e-01 1.04e+01 angle pdb=" C GLU B 258 " pdb=" N LYS B 259 " pdb=" CA LYS B 259 " ideal model delta sigma weight residual 121.14 115.54 5.60 1.75e+00 3.27e-01 1.02e+01 angle pdb=" C GLU A 258 " pdb=" N LYS A 259 " pdb=" CA LYS A 259 " ideal model delta sigma weight residual 121.14 115.55 5.59 1.75e+00 3.27e-01 1.02e+01 angle pdb=" C GLU G 258 " pdb=" N LYS G 259 " pdb=" CA LYS G 259 " ideal model delta sigma weight residual 121.14 115.56 5.58 1.75e+00 3.27e-01 1.02e+01 ... (remaining 19196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 7475 14.99 - 29.99: 881 29.99 - 44.98: 156 44.98 - 59.97: 21 59.97 - 74.97: 42 Dihedral angle restraints: 8575 sinusoidal: 3444 harmonic: 5131 Sorted by residual: dihedral pdb=" CA PRO C 286 " pdb=" C PRO C 286 " pdb=" N PRO C 287 " pdb=" CA PRO C 287 " ideal model delta harmonic sigma weight residual -180.00 -148.65 -31.35 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA PRO E 286 " pdb=" C PRO E 286 " pdb=" N PRO E 287 " pdb=" CA PRO E 287 " ideal model delta harmonic sigma weight residual -180.00 -148.70 -31.30 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA PRO D 286 " pdb=" C PRO D 286 " pdb=" N PRO D 287 " pdb=" CA PRO D 287 " ideal model delta harmonic sigma weight residual -180.00 -148.71 -31.29 0 5.00e+00 4.00e-02 3.92e+01 ... (remaining 8572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1238 0.055 - 0.110: 624 0.110 - 0.165: 161 0.165 - 0.221: 21 0.221 - 0.276: 7 Chirality restraints: 2051 Sorted by residual: chirality pdb=" CA GLU A 222 " pdb=" N GLU A 222 " pdb=" C GLU A 222 " pdb=" CB GLU A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU E 222 " pdb=" N GLU E 222 " pdb=" C GLU E 222 " pdb=" CB GLU E 222 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU F 222 " pdb=" N GLU F 222 " pdb=" C GLU F 222 " pdb=" CB GLU F 222 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2048 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 286 " 0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO D 287 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 287 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 286 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.93e+00 pdb=" N PRO E 287 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 287 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 286 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO A 287 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.037 5.00e-02 4.00e+02 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.60: 422 2.60 - 3.10: 10723 3.10 - 3.60: 17626 3.60 - 4.10: 22963 4.10 - 4.60: 36459 Nonbonded interactions: 88193 Sorted by model distance: nonbonded pdb=" HB THR D 262 " pdb=" HG1 THR D 262 " model vdw 2.103 1.816 nonbonded pdb=" HB THR E 262 " pdb=" HG1 THR E 262 " model vdw 2.105 1.816 nonbonded pdb=" HB THR C 262 " pdb=" HG1 THR C 262 " model vdw 2.105 1.816 nonbonded pdb=" HB THR B 262 " pdb=" HG1 THR B 262 " model vdw 2.119 1.816 nonbonded pdb=" HB2 GLU F 258 " pdb=" HG3 GLU F 258 " model vdw 2.133 1.952 ... (remaining 88188 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.280 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: 0.370 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 28.020 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.016 0.075 13853 Z= 1.029 Angle : 1.063 11.313 18851 Z= 0.565 Chirality : 0.067 0.276 2051 Planarity : 0.008 0.075 2555 Dihedral : 14.069 74.966 5194 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 2.06 (0.20), residues: 1715 helix: 1.67 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 0.86 (0.30), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP C 156 HIS 0.008 0.004 HIS D 216 PHE 0.051 0.006 PHE F 130 TYR 0.029 0.006 TYR G 264 ARG 0.017 0.002 ARG E 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.568 Fit side-chains REVERT: B 221 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7619 (ttm170) REVERT: C 25 MET cc_start: 0.8513 (mtm) cc_final: 0.8097 (mtp) REVERT: C 130 PHE cc_start: 0.8261 (m-80) cc_final: 0.8049 (m-80) REVERT: D 245 GLN cc_start: 0.7345 (mm110) cc_final: 0.7037 (tp40) REVERT: F 11 GLN cc_start: 0.7993 (tt0) cc_final: 0.7760 (pm20) REVERT: G 205 MET cc_start: 0.8410 (ttp) cc_final: 0.8171 (ttp) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 1.6999 time to fit residues: 676.7652 Evaluate side-chains 251 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 0.0010 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 ASN A 245 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN C 11 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN E 254 GLN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN G 245 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13853 Z= 0.142 Angle : 0.489 7.517 18851 Z= 0.255 Chirality : 0.034 0.124 2051 Planarity : 0.005 0.062 2555 Dihedral : 3.935 14.495 1883 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.80 % Allowed : 10.89 % Favored : 87.30 % 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: 4.34 (0.20), residues: 1715 helix: 3.68 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.92 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 156 HIS 0.003 0.001 HIS A 216 PHE 0.013 0.002 PHE C 152 TYR 0.016 0.002 TYR C 264 ARG 0.004 0.001 ARG G 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 319 time to evaluate : 1.701 Fit side-chains revert: symmetry clash REVERT: B 134 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8515 (ttpp) REVERT: C 25 MET cc_start: 0.8451 (mtm) cc_final: 0.8044 (mtp) REVERT: C 263 GLU cc_start: 0.8001 (tp30) cc_final: 0.7798 (tp30) REVERT: D 134 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8541 (ttpp) REVERT: E 81 TYR cc_start: 0.7803 (m-80) cc_final: 0.7592 (m-80) REVERT: F 233 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: G 205 MET cc_start: 0.8377 (ttp) cc_final: 0.8070 (ttp) outliers start: 25 outliers final: 10 residues processed: 335 average time/residue: 1.4375 time to fit residues: 519.5821 Evaluate side-chains 288 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 275 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 233 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 0.0000 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN B 11 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13853 Z= 0.114 Angle : 0.422 6.160 18851 Z= 0.214 Chirality : 0.032 0.120 2051 Planarity : 0.004 0.048 2555 Dihedral : 3.458 11.901 1883 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.95 % Allowed : 13.20 % Favored : 84.85 % 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: 5.17 (0.21), residues: 1715 helix: 4.34 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.15 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 156 HIS 0.003 0.001 HIS A 216 PHE 0.014 0.002 PHE B 152 TYR 0.011 0.001 TYR G 236 ARG 0.002 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 302 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: B 134 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8550 (ttpp) REVERT: C 25 MET cc_start: 0.8455 (mtm) cc_final: 0.8034 (mtp) REVERT: D 134 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8672 (mtpt) REVERT: F 233 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7069 (tt0) REVERT: G 25 MET cc_start: 0.8565 (mtp) cc_final: 0.8303 (mtp) REVERT: G 134 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8511 (ttpp) REVERT: G 205 MET cc_start: 0.8374 (ttp) cc_final: 0.8035 (ttp) REVERT: G 271 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7798 (mm-30) outliers start: 27 outliers final: 10 residues processed: 317 average time/residue: 1.4251 time to fit residues: 486.6138 Evaluate side-chains 297 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 283 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 80 optimal weight: 0.0270 chunk 145 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13853 Z= 0.191 Angle : 0.458 5.178 18851 Z= 0.237 Chirality : 0.034 0.121 2051 Planarity : 0.004 0.047 2555 Dihedral : 3.475 11.325 1883 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.25 % Allowed : 12.84 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.21), residues: 1715 helix: 3.97 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : 1.11 (0.32), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 156 HIS 0.006 0.002 HIS B 216 PHE 0.018 0.002 PHE B 152 TYR 0.014 0.002 TYR D 236 ARG 0.004 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 274 time to evaluate : 1.602 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8519 (ttpp) REVERT: B 134 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8581 (ttpp) REVERT: C 25 MET cc_start: 0.8434 (mtm) cc_final: 0.8005 (mtp) REVERT: D 134 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8569 (ttpp) REVERT: F 11 GLN cc_start: 0.6383 (pm20) cc_final: 0.5648 (pm20) REVERT: F 233 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7059 (tt0) REVERT: G 134 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8550 (ttpp) REVERT: G 205 MET cc_start: 0.8380 (ttp) cc_final: 0.8040 (ttp) REVERT: G 271 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7775 (mm-30) outliers start: 45 outliers final: 19 residues processed: 298 average time/residue: 1.5011 time to fit residues: 483.6552 Evaluate side-chains 292 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 268 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 233 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 8.9990 chunk 92 optimal weight: 0.0470 chunk 2 optimal weight: 0.0970 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 overall best weight: 3.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN B 48 GLN B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN F 48 GLN F 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13853 Z= 0.355 Angle : 0.568 6.033 18851 Z= 0.297 Chirality : 0.039 0.116 2051 Planarity : 0.006 0.059 2555 Dihedral : 3.800 13.851 1883 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.90 % Allowed : 13.28 % Favored : 82.83 % 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: 4.55 (0.21), residues: 1715 helix: 3.78 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.18 (0.32), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 156 HIS 0.008 0.002 HIS B 216 PHE 0.023 0.003 PHE B 152 TYR 0.022 0.003 TYR G 236 ARG 0.005 0.001 ARG E 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 260 time to evaluate : 1.544 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8571 (ttpp) REVERT: C 25 MET cc_start: 0.8493 (mtm) cc_final: 0.8036 (mtp) REVERT: D 134 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8550 (ttpp) REVERT: E 81 TYR cc_start: 0.7759 (m-80) cc_final: 0.7484 (m-80) REVERT: F 11 GLN cc_start: 0.6574 (pm20) cc_final: 0.5862 (pm20) REVERT: F 233 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: G 134 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8572 (ttpp) REVERT: G 205 MET cc_start: 0.8396 (ttp) cc_final: 0.8123 (ttp) REVERT: G 271 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7759 (mm-30) outliers start: 54 outliers final: 26 residues processed: 289 average time/residue: 1.5409 time to fit residues: 478.0651 Evaluate side-chains 289 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 259 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 233 GLU Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9990 chunk 146 optimal weight: 0.0970 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 13853 Z= 0.124 Angle : 0.418 5.023 18851 Z= 0.216 Chirality : 0.033 0.125 2051 Planarity : 0.004 0.042 2555 Dihedral : 3.385 11.469 1883 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.74 % Allowed : 15.15 % Favored : 82.11 % 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: 4.92 (0.21), residues: 1715 helix: 4.04 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : 1.08 (0.32), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 156 HIS 0.003 0.001 HIS F 216 PHE 0.014 0.001 PHE C 152 TYR 0.013 0.001 TYR G 236 ARG 0.004 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 284 time to evaluate : 1.537 Fit side-chains REVERT: A 134 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8515 (ttpp) REVERT: C 25 MET cc_start: 0.8466 (mtm) cc_final: 0.8049 (mtp) REVERT: D 134 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8588 (ttpp) REVERT: E 233 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7065 (tt0) REVERT: F 69 ARG cc_start: 0.8645 (mtt180) cc_final: 0.8444 (mtt-85) REVERT: G 134 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8548 (ttpp) REVERT: G 205 MET cc_start: 0.8367 (ttp) cc_final: 0.8060 (ttp) outliers start: 38 outliers final: 15 residues processed: 302 average time/residue: 1.4889 time to fit residues: 483.4407 Evaluate side-chains 292 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 273 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 0.0470 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 265 ASN B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13853 Z= 0.185 Angle : 0.452 5.418 18851 Z= 0.234 Chirality : 0.034 0.121 2051 Planarity : 0.004 0.045 2555 Dihedral : 3.401 12.050 1883 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.38 % Allowed : 16.38 % Favored : 81.24 % 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: 4.89 (0.21), residues: 1715 helix: 3.98 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : 1.14 (0.32), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 156 HIS 0.005 0.001 HIS B 216 PHE 0.018 0.002 PHE B 152 TYR 0.018 0.002 TYR G 236 ARG 0.003 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 269 time to evaluate : 1.790 Fit side-chains REVERT: A 134 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8534 (ttpp) REVERT: C 25 MET cc_start: 0.8460 (mtm) cc_final: 0.8051 (mtp) REVERT: D 134 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8570 (ttpp) REVERT: E 233 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7102 (tt0) REVERT: F 11 GLN cc_start: 0.6360 (pm20) cc_final: 0.5664 (pm20) REVERT: F 233 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: G 134 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8570 (ttpp) REVERT: G 205 MET cc_start: 0.8375 (ttp) cc_final: 0.8065 (ttp) outliers start: 33 outliers final: 14 residues processed: 287 average time/residue: 1.5308 time to fit residues: 472.3214 Evaluate side-chains 287 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 268 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 13853 Z= 0.121 Angle : 0.407 4.693 18851 Z= 0.209 Chirality : 0.033 0.122 2051 Planarity : 0.004 0.036 2555 Dihedral : 3.218 10.759 1883 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.66 % Allowed : 17.17 % Favored : 81.17 % 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: 5.22 (0.21), residues: 1715 helix: 4.29 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 1.19 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 156 HIS 0.003 0.001 HIS F 216 PHE 0.014 0.002 PHE C 152 TYR 0.017 0.001 TYR G 236 ARG 0.003 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 277 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8490 (ttpp) REVERT: C 25 MET cc_start: 0.8439 (mtm) cc_final: 0.8022 (mtp) REVERT: D 134 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8688 (mtpt) REVERT: E 233 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: G 205 MET cc_start: 0.8363 (ttp) cc_final: 0.8064 (ttp) outliers start: 23 outliers final: 12 residues processed: 289 average time/residue: 1.4761 time to fit residues: 459.7099 Evaluate side-chains 288 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 273 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 142 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 265 ASN B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13853 Z= 0.146 Angle : 0.422 4.916 18851 Z= 0.216 Chirality : 0.033 0.121 2051 Planarity : 0.004 0.036 2555 Dihedral : 3.216 10.759 1883 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.80 % Allowed : 16.96 % Favored : 81.24 % 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: 5.17 (0.21), residues: 1715 helix: 4.25 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 1.18 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 156 HIS 0.004 0.001 HIS F 216 PHE 0.017 0.002 PHE C 152 TYR 0.027 0.002 TYR F 236 ARG 0.004 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 274 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8488 (ttpp) REVERT: C 25 MET cc_start: 0.8438 (mtm) cc_final: 0.8024 (mtp) REVERT: D 134 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8700 (mtpt) REVERT: E 233 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: F 11 GLN cc_start: 0.6332 (pm20) cc_final: 0.5512 (pm20) REVERT: F 233 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: G 205 MET cc_start: 0.8371 (ttp) cc_final: 0.8067 (ttp) outliers start: 25 outliers final: 12 residues processed: 285 average time/residue: 1.5457 time to fit residues: 472.6764 Evaluate side-chains 293 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 277 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 265 ASN B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13853 Z= 0.139 Angle : 0.417 4.815 18851 Z= 0.214 Chirality : 0.033 0.122 2051 Planarity : 0.004 0.035 2555 Dihedral : 3.173 12.986 1883 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.30 % Allowed : 17.46 % Favored : 81.24 % 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: 5.22 (0.21), residues: 1715 helix: 4.28 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 1.21 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 156 HIS 0.004 0.001 HIS F 216 PHE 0.016 0.002 PHE C 152 TYR 0.024 0.001 TYR F 236 ARG 0.004 0.000 ARG F 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 271 time to evaluate : 1.629 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8479 (ttpp) REVERT: C 25 MET cc_start: 0.8423 (mtm) cc_final: 0.8002 (mtp) REVERT: E 233 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: F 233 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: G 205 MET cc_start: 0.8364 (ttp) cc_final: 0.8061 (ttp) outliers start: 18 outliers final: 12 residues processed: 279 average time/residue: 1.5395 time to fit residues: 461.6388 Evaluate side-chains 287 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 272 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 8.9990 chunk 122 optimal weight: 0.0570 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 133 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.085044 restraints weight = 22437.391| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.11 r_work: 0.3105 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 13853 Z= 0.103 Angle : 0.388 4.601 18851 Z= 0.196 Chirality : 0.032 0.122 2051 Planarity : 0.003 0.028 2555 Dihedral : 3.018 10.472 1883 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.37 % Allowed : 17.60 % Favored : 81.02 % 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: 5.41 (0.21), residues: 1715 helix: 4.42 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : 1.25 (0.32), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 156 HIS 0.003 0.001 HIS F 216 PHE 0.013 0.001 PHE C 152 TYR 0.023 0.001 TYR F 236 ARG 0.004 0.000 ARG F 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7020.07 seconds wall clock time: 122 minutes 32.07 seconds (7352.07 seconds total)