Starting phenix.real_space_refine on Thu Nov 14 02:06:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zng_60270/11_2024/8zng_60270.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zng_60270/11_2024/8zng_60270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zng_60270/11_2024/8zng_60270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zng_60270/11_2024/8zng_60270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zng_60270/11_2024/8zng_60270.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zng_60270/11_2024/8zng_60270.cif" } resolution = 2.5 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= 0.002 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 P 3 5.49 5 S 14 5.16 5 C 2115 2.51 5 N 567 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3347 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Conformer: "B" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} bond proxies already assigned to first conformer: 3322 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 74 Unusual residues: {'AKG': 1, 'NDP': 1} Classifications: {'undetermined': 2, 'water': 16} Link IDs: {None: 17} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 187 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 187 " occ=0.50 Time building chain proxies: 4.42, per 1000 atoms: 1.32 Number of scatterers: 3347 At special positions: 0 Unit cell: (65.424, 63.168, 70.688, 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 14 16.00 P 3 15.00 O 648 8.00 N 567 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.95 Conformation dependent library (CDL) restraints added in 758.7 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 55.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.588A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.708A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.800A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.801A pdb=" N LEU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.975A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 391 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.683A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.683A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 7.626A pdb=" N VAL A 217 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 242 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 555 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: 1.31 Time building geometry restraints manager: 1.02 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: 1086 1.34 - 1.46: 617 1.46 - 1.58: 1672 1.58 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3407 Sorted by residual: bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.614 0.219 3.80e-02 6.93e+02 3.33e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.603 0.154 3.50e-02 8.16e+02 1.95e+01 bond pdb=" C2B NDP A 500 " pdb=" O2B NDP A 500 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.90e-02 1.19e+03 1.03e+01 bond pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 1.368 1.448 -0.080 3.20e-02 9.77e+02 6.23e+00 bond pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.513 1.492 0.021 1.00e-02 1.00e+04 4.47e+00 ... (remaining 3402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 4598 4.67 - 9.34: 25 9.34 - 14.02: 1 14.02 - 18.69: 1 18.69 - 23.36: 1 Bond angle restraints: 4626 Sorted by residual: angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 131.10 -23.36 1.95e+00 2.62e-01 1.43e+02 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 117.90 -14.06 1.91e+00 2.73e-01 5.39e+01 angle pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 104.93 117.39 -12.46 2.66e+00 1.41e-01 2.20e+01 angle pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 100.52 109.31 -8.79 1.91e+00 2.74e-01 2.11e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 112.22 5.24 1.17e+00 7.36e-01 2.02e+01 ... (remaining 4621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 1929 36.00 - 71.99: 84 71.99 - 107.99: 8 107.99 - 143.98: 0 143.98 - 179.98: 1 Dihedral angle restraints: 2022 sinusoidal: 829 harmonic: 1193 Sorted by residual: dihedral pdb=" CD BARG A 187 " pdb=" NE BARG A 187 " pdb=" CZ BARG A 187 " pdb=" NH1BARG A 187 " ideal model delta sinusoidal sigma weight residual 0.00 179.98 -179.98 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 67.30 107.74 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" CA ASP A 307 " pdb=" CB ASP A 307 " pdb=" CG ASP A 307 " pdb=" OD1 ASP A 307 " ideal model delta sinusoidal sigma weight residual -30.00 -86.71 56.71 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 2019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 390 0.050 - 0.100: 81 0.100 - 0.150: 27 0.150 - 0.200: 2 0.200 - 0.249: 2 Chirality restraints: 502 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.46 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE A 4 " pdb=" CA ILE A 4 " pdb=" CG1 ILE A 4 " pdb=" CG2 ILE A 4 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.40 0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 499 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.085 2.00e-02 2.50e+03 5.31e-02 3.52e+01 pdb=" C3N NDP A 500 " 0.015 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " 0.013 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.046 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 273 " -0.050 5.00e-02 4.00e+02 7.43e-02 8.84e+00 pdb=" N PRO A 274 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 150 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.026 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1356 2.93 - 3.42: 3427 3.42 - 3.92: 6115 3.92 - 4.41: 6992 4.41 - 4.90: 11116 Nonbonded interactions: 29006 Sorted by model distance: nonbonded pdb=" OD1 ASP A 48 " pdb=" OG SER A 50 " model vdw 2.439 3.040 nonbonded pdb=" O LEU A 99 " pdb=" O HOH A 601 " model vdw 2.439 3.040 nonbonded pdb=" OE1 GLU A 354 " pdb=" O HOH A 602 " model vdw 2.481 3.040 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.535 3.120 nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 601 " model vdw 2.549 3.120 ... (remaining 29001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.810 Find NCS groups from input model: 0.050 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:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 : 0.007 0.219 3407 Z= 0.438 Angle : 0.920 23.360 4626 Z= 0.499 Chirality : 0.048 0.249 502 Planarity : 0.006 0.074 592 Dihedral : 19.319 179.977 1262 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.24 % Allowed : 17.94 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.43), residues: 417 helix: 2.31 (0.38), residues: 200 sheet: -0.02 (0.69), residues: 64 loop : -0.75 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 PHE 0.013 0.002 PHE A 381 TYR 0.012 0.001 TYR A 408 ARG 0.002 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.405 Fit side-chains REVERT: A 388 HIS cc_start: 0.9048 (OUTLIER) cc_final: 0.8420 (p-80) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 1.6467 time to fit residues: 126.2457 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 419 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3407 Z= 0.293 Angle : 0.557 7.786 4626 Z= 0.295 Chirality : 0.047 0.194 502 Planarity : 0.005 0.048 592 Dihedral : 11.777 179.665 485 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.06 % Allowed : 21.18 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.41), residues: 417 helix: 2.12 (0.36), residues: 203 sheet: 0.61 (0.79), residues: 54 loop : -1.20 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 382 HIS 0.005 0.002 HIS A 388 PHE 0.014 0.002 PHE A 341 TYR 0.016 0.002 TYR A 363 ARG 0.004 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.406 Fit side-chains REVERT: A 265 ARG cc_start: 0.7414 (ttp-170) cc_final: 0.7092 (ttm170) outliers start: 6 outliers final: 3 residues processed: 60 average time/residue: 1.5688 time to fit residues: 96.3552 Evaluate side-chains 51 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3407 Z= 0.263 Angle : 0.526 7.374 4626 Z= 0.278 Chirality : 0.046 0.193 502 Planarity : 0.005 0.046 592 Dihedral : 11.037 179.656 474 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.94 % Allowed : 19.41 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.41), residues: 417 helix: 1.97 (0.36), residues: 204 sheet: 0.52 (0.79), residues: 56 loop : -1.27 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.014 0.002 PHE A 381 TYR 0.016 0.002 TYR A 363 ARG 0.003 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.320 Fit side-chains REVERT: A 290 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6998 (t70) outliers start: 9 outliers final: 3 residues processed: 59 average time/residue: 1.7042 time to fit residues: 102.9630 Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3407 Z= 0.149 Angle : 0.469 6.275 4626 Z= 0.245 Chirality : 0.043 0.197 502 Planarity : 0.004 0.046 592 Dihedral : 10.524 179.902 472 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.65 % Allowed : 19.71 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.42), residues: 417 helix: 2.16 (0.36), residues: 204 sheet: 0.60 (0.79), residues: 56 loop : -1.18 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.012 0.001 PHE A 381 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.342 Fit side-chains REVERT: A 265 ARG cc_start: 0.7406 (ttp-170) cc_final: 0.7108 (mtt-85) REVERT: A 290 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6978 (t70) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 1.6934 time to fit residues: 90.2360 Evaluate side-chains 50 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3407 Z= 0.166 Angle : 0.476 6.221 4626 Z= 0.250 Chirality : 0.043 0.202 502 Planarity : 0.004 0.046 592 Dihedral : 10.380 179.874 471 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.35 % Allowed : 20.29 % Favored : 77.35 % 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: 1.13 (0.42), residues: 417 helix: 2.17 (0.36), residues: 204 sheet: 0.71 (0.80), residues: 56 loop : -1.22 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.336 Fit side-chains REVERT: A 265 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7049 (mtt-85) REVERT: A 290 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6927 (t70) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 1.6797 time to fit residues: 84.3099 Evaluate side-chains 52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 overall best weight: 0.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3407 Z= 0.151 Angle : 0.467 5.936 4626 Z= 0.244 Chirality : 0.043 0.201 502 Planarity : 0.004 0.046 592 Dihedral : 10.208 179.916 471 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.35 % Allowed : 19.71 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.42), residues: 417 helix: 2.21 (0.36), residues: 204 sheet: 0.65 (0.78), residues: 56 loop : -1.18 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.350 Fit side-chains REVERT: A 265 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7152 (mtt-85) REVERT: A 290 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6901 (t70) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 1.6174 time to fit residues: 91.1235 Evaluate side-chains 52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3407 Z= 0.147 Angle : 0.469 5.801 4626 Z= 0.244 Chirality : 0.043 0.199 502 Planarity : 0.004 0.045 592 Dihedral : 10.034 179.956 471 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.35 % Allowed : 20.00 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.42), residues: 417 helix: 2.24 (0.36), residues: 204 sheet: 0.62 (0.77), residues: 56 loop : -1.10 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.406 Fit side-chains REVERT: A 265 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7170 (mtt-85) REVERT: A 290 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6931 (t70) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 1.6728 time to fit residues: 85.6838 Evaluate side-chains 54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3407 Z= 0.148 Angle : 0.484 6.533 4626 Z= 0.249 Chirality : 0.043 0.199 502 Planarity : 0.004 0.046 592 Dihedral : 9.924 179.921 471 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.35 % Allowed : 20.00 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.42), residues: 417 helix: 2.07 (0.36), residues: 209 sheet: 0.25 (0.70), residues: 66 loop : -1.06 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.384 Fit side-chains REVERT: A 265 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7177 (mtt-85) REVERT: A 290 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6925 (t70) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 1.6218 time to fit residues: 86.4065 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 3407 Z= 0.204 Angle : 0.625 15.704 4626 Z= 0.335 Chirality : 0.048 0.493 502 Planarity : 0.005 0.077 592 Dihedral : 9.888 179.944 471 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.35 % Allowed : 20.00 % Favored : 77.65 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.42), residues: 417 helix: 2.09 (0.36), residues: 209 sheet: 0.25 (0.70), residues: 66 loop : -1.00 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.441 Fit side-chains REVERT: A 265 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7211 (mtt-85) REVERT: A 290 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6930 (t70) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 1.5409 time to fit residues: 80.5724 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.0870 chunk 25 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3407 Z= 0.131 Angle : 0.473 6.808 4626 Z= 0.242 Chirality : 0.042 0.195 502 Planarity : 0.004 0.046 592 Dihedral : 9.800 179.974 471 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.35 % Allowed : 20.00 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.42), residues: 417 helix: 2.16 (0.36), residues: 209 sheet: 0.11 (0.70), residues: 65 loop : -0.88 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.006 0.001 TYR A 408 ARG 0.001 0.000 ARG A 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.383 Fit side-chains REVERT: A 265 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7197 (mtt-85) REVERT: A 290 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6906 (t70) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 1.5563 time to fit residues: 87.6975 Evaluate side-chains 55 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.086481 restraints weight = 7979.278| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.25 r_work: 0.2735 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3407 Z= 0.151 Angle : 0.489 7.784 4626 Z= 0.249 Chirality : 0.043 0.196 502 Planarity : 0.004 0.045 592 Dihedral : 9.803 179.917 471 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.76 % Allowed : 21.18 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.42), residues: 417 helix: 2.14 (0.36), residues: 209 sheet: 0.16 (0.70), residues: 65 loop : -0.89 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2049.04 seconds wall clock time: 37 minutes 29.86 seconds (2249.86 seconds total)