Starting phenix.real_space_refine on Thu Nov 14 02:09:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/11_2024/8znc_60267.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/11_2024/8znc_60267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/11_2024/8znc_60267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/11_2024/8znc_60267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/11_2024/8znc_60267.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/11_2024/8znc_60267.cif" } resolution = 2.41 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 2118 2.51 5 N 565 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 3356 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: 3321 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 83 Unusual residues: {'AKG': 1, 'NDP': 1, 'NH4': 1} Classifications: {'undetermined': 3, 'water': 24} Link IDs: {None: 26} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 89 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 89 " occ=0.50 Time building chain proxies: 4.41, per 1000 atoms: 1.31 Number of scatterers: 3356 At special positions: 0 Unit cell: (66.176, 63.92, 72.192, 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 656 8.00 N 565 7.00 C 2118 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: 1.48 Conformation dependent library (CDL) restraints added in 814.7 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: 18 helices and 2 sheets defined 56.0% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.933A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.692A 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 169 through 174 removed outlier: 3.583A pdb=" N GLY A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.741A 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 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.532A pdb=" N GLU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 334 " --> pdb=" O LEU A 330 " (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 392 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: 4.663A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 3.536A pdb=" N THR A 277 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE A 215 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL A 242 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 217 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 293 " --> pdb=" O ALA A 216 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 538 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: 1.17 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 865 1.33 - 1.45: 607 1.45 - 1.57: 1904 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3408 Sorted by residual: bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.611 0.222 3.80e-02 6.93e+02 3.40e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.601 0.156 3.50e-02 8.16e+02 1.98e+01 bond pdb=" C1 AKG A 502 " pdb=" O2 AKG A 502 " ideal model delta sigma weight residual 1.239 1.308 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C2B NDP A 501 " pdb=" O2B NDP A 501 " ideal model delta sigma weight residual 1.330 1.424 -0.094 2.90e-02 1.19e+03 1.06e+01 bond pdb=" C LYS A 418 " pdb=" N LYS A 419 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.40e-02 5.10e+03 8.23e+00 ... (remaining 3403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.59: 4611 5.59 - 11.18: 14 11.18 - 16.78: 2 16.78 - 22.37: 0 22.37 - 27.96: 1 Bond angle restraints: 4628 Sorted by residual: angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 135.70 -27.96 1.95e+00 2.62e-01 2.05e+02 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 119.42 -15.58 1.91e+00 2.73e-01 6.62e+01 angle pdb=" O1X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.46 111.72 5.74 1.17e+00 7.36e-01 2.42e+01 angle pdb=" O2N NDP A 501 " pdb=" PN NDP A 501 " pdb=" O5D NDP A 501 " ideal model delta sigma weight residual 100.52 109.00 -8.48 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C5D NDP A 501 " pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 104.93 116.71 -11.78 2.66e+00 1.41e-01 1.96e+01 ... (remaining 4623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 1696 17.52 - 35.03: 213 35.03 - 52.55: 73 52.55 - 70.06: 27 70.06 - 87.58: 10 Dihedral angle restraints: 2019 sinusoidal: 826 harmonic: 1193 Sorted by residual: dihedral pdb=" CA THR A 148 " pdb=" C THR A 148 " pdb=" N ASN A 149 " pdb=" CA ASN A 149 " ideal model delta harmonic sigma weight residual -180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP A 290 " pdb=" CB ASP A 290 " pdb=" CG ASP A 290 " pdb=" OD1 ASP A 290 " ideal model delta sinusoidal sigma weight residual -30.00 -88.81 58.81 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP A 272 " pdb=" CB ASP A 272 " pdb=" CG ASP A 272 " pdb=" OD1 ASP A 272 " ideal model delta sinusoidal sigma weight residual -30.00 -88.28 58.28 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 389 0.050 - 0.099: 87 0.099 - 0.149: 23 0.149 - 0.199: 1 0.199 - 0.248: 2 Chirality restraints: 502 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.47 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C1B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" N9A NDP A 501 " pdb=" O4B NDP A 501 " both_signs ideal model delta sigma weight residual False 2.59 2.37 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" C4B NDP A 501 " pdb=" O3B NDP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.58 -0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 499 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 501 " -0.067 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" C3N NDP A 501 " -0.015 2.00e-02 2.50e+03 pdb=" C4N NDP A 501 " -0.010 2.00e-02 2.50e+03 pdb=" C7N NDP A 501 " 0.038 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 501 " 0.013 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C5N NDP A 501 " -0.027 2.00e-02 2.50e+03 pdb=" C6N NDP A 501 " 0.028 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 187 " 0.167 9.50e-02 1.11e+02 7.48e-02 3.44e+00 pdb=" NE ARG A 187 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 187 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 187 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 187 " 0.006 2.00e-02 2.50e+03 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1291 2.91 - 3.40: 3410 3.40 - 3.90: 6166 3.90 - 4.40: 6974 4.40 - 4.90: 11155 Nonbonded interactions: 28996 Sorted by model distance: nonbonded pdb=" OE1 GLU A 383 " pdb=" NH2 ARG A 406 " model vdw 2.408 3.120 nonbonded pdb=" OD1 ASP A 5 " pdb=" OG SER A 81 " model vdw 2.423 3.040 nonbonded pdb=" NE ARG A 73 " pdb=" OE1 GLU A 78 " model vdw 2.434 3.120 nonbonded pdb=" ND1 HIS A 388 " pdb=" O ILE A 393 " model vdw 2.446 3.120 nonbonded pdb=" NZ LYS A 69 " pdb=" OG1 THR A 175 " model vdw 2.506 3.120 ... (remaining 28991 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: 0.860 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.030 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:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 0.222 3408 Z= 0.516 Angle : 0.967 27.959 4628 Z= 0.534 Chirality : 0.047 0.248 502 Planarity : 0.006 0.075 592 Dihedral : 19.343 87.579 1259 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.76 % Allowed : 25.00 % Favored : 73.24 % 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: 0.66 (0.42), residues: 417 helix: 1.80 (0.36), residues: 207 sheet: -0.68 (0.68), residues: 68 loop : -1.01 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 364 HIS 0.009 0.002 HIS A 394 PHE 0.012 0.002 PHE A 381 TYR 0.015 0.001 TYR A 363 ARG 0.002 0.000 ARG A 118 *********************** 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 73 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.390 Fit side-chains REVERT: A 213 LYS cc_start: 0.7494 (mmtp) cc_final: 0.7268 (mmmm) REVERT: A 272 ASP cc_start: 0.7401 (m-30) cc_final: 0.7057 (m-30) REVERT: A 312 LYS cc_start: 0.7503 (mttm) cc_final: 0.7293 (mptt) REVERT: A 333 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7782 (mttp) REVERT: A 335 ILE cc_start: 0.8457 (mt) cc_final: 0.8127 (mm) outliers start: 6 outliers final: 2 residues processed: 71 average time/residue: 1.4732 time to fit residues: 107.2588 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 220 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.8718 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3408 Z= 0.205 Angle : 0.525 6.558 4628 Z= 0.277 Chirality : 0.043 0.130 502 Planarity : 0.004 0.046 592 Dihedral : 6.441 55.208 471 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.29 % Allowed : 22.06 % Favored : 72.65 % 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: 0.89 (0.42), residues: 417 helix: 1.98 (0.35), residues: 211 sheet: -0.54 (0.72), residues: 62 loop : -0.97 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 364 HIS 0.004 0.001 HIS A 388 PHE 0.012 0.002 PHE A 381 TYR 0.012 0.001 TYR A 363 ARG 0.002 0.000 ARG A 118 *********************** 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 79 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.431 Fit side-chains REVERT: A 272 ASP cc_start: 0.7500 (m-30) cc_final: 0.7097 (m-30) REVERT: A 286 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: A 312 LYS cc_start: 0.7567 (mttm) cc_final: 0.7345 (mptt) REVERT: A 333 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7947 (mtpp) REVERT: A 335 ILE cc_start: 0.8516 (mt) cc_final: 0.8193 (mm) REVERT: A 376 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.7510 (mptp) outliers start: 18 outliers final: 8 residues processed: 75 average time/residue: 1.5310 time to fit residues: 117.6018 Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3408 Z= 0.198 Angle : 0.529 8.690 4628 Z= 0.272 Chirality : 0.043 0.132 502 Planarity : 0.004 0.047 592 Dihedral : 6.300 55.066 470 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.53 % Allowed : 22.94 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.41), residues: 417 helix: 2.04 (0.35), residues: 211 sheet: -0.41 (0.72), residues: 62 loop : -1.01 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.004 0.001 HIS A 388 PHE 0.011 0.002 PHE A 381 TYR 0.013 0.001 TYR A 363 ARG 0.002 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 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.378 Fit side-chains REVERT: A 272 ASP cc_start: 0.7537 (m-30) cc_final: 0.7188 (m-30) REVERT: A 286 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: A 335 ILE cc_start: 0.8524 (mt) cc_final: 0.8212 (mm) REVERT: A 376 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.7519 (mptp) outliers start: 12 outliers final: 3 residues processed: 65 average time/residue: 1.5993 time to fit residues: 106.6374 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS 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: 4.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 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 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3408 Z= 0.156 Angle : 0.487 8.014 4628 Z= 0.251 Chirality : 0.042 0.130 502 Planarity : 0.004 0.047 592 Dihedral : 5.372 57.575 468 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 24.41 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.42), residues: 417 helix: 2.26 (0.35), residues: 211 sheet: -0.27 (0.72), residues: 62 loop : -0.98 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.002 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 406 *********************** 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 64 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.390 Fit side-chains REVERT: A 272 ASP cc_start: 0.7584 (m-30) cc_final: 0.7222 (m-30) REVERT: A 286 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: A 335 ILE cc_start: 0.8410 (mt) cc_final: 0.8079 (mm) REVERT: A 376 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.7567 (mptp) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 1.5174 time to fit residues: 99.5236 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS 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: 0.0870 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3408 Z= 0.151 Angle : 0.488 7.514 4628 Z= 0.249 Chirality : 0.042 0.127 502 Planarity : 0.004 0.048 592 Dihedral : 5.244 57.056 468 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.47 % Allowed : 25.29 % Favored : 73.24 % 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: 1.28 (0.42), residues: 417 helix: 2.31 (0.35), residues: 211 sheet: -0.21 (0.72), residues: 62 loop : -0.89 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 331 *********************** 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 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.403 Fit side-chains REVERT: A 272 ASP cc_start: 0.7505 (m-30) cc_final: 0.7218 (m-30) REVERT: A 286 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: A 300 VAL cc_start: 0.8297 (m) cc_final: 0.8071 (p) REVERT: A 335 ILE cc_start: 0.8424 (mt) cc_final: 0.8116 (mm) REVERT: A 376 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.7594 (mptp) outliers start: 5 outliers final: 2 residues processed: 62 average time/residue: 1.4323 time to fit residues: 91.0921 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3408 Z= 0.226 Angle : 0.529 7.223 4628 Z= 0.274 Chirality : 0.044 0.131 502 Planarity : 0.005 0.048 592 Dihedral : 5.460 53.940 468 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.06 % Allowed : 25.00 % Favored : 72.94 % 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: 1.15 (0.41), residues: 417 helix: 2.19 (0.35), residues: 211 sheet: -0.29 (0.71), residues: 62 loop : -0.91 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 263 HIS 0.004 0.001 HIS A 388 PHE 0.012 0.002 PHE A 381 TYR 0.014 0.001 TYR A 363 ARG 0.002 0.000 ARG A 165 *********************** 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 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.414 Fit side-chains REVERT: A 272 ASP cc_start: 0.7515 (m-30) cc_final: 0.7190 (m-30) REVERT: A 286 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: A 327 ASP cc_start: 0.7800 (m-30) cc_final: 0.7478 (m-30) REVERT: A 335 ILE cc_start: 0.8465 (mt) cc_final: 0.8148 (mm) REVERT: A 376 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.7516 (mptp) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 1.4988 time to fit residues: 95.2659 Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 25 optimal weight: 5.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3408 Z= 0.245 Angle : 0.547 7.070 4628 Z= 0.284 Chirality : 0.044 0.132 502 Planarity : 0.005 0.048 592 Dihedral : 5.537 52.974 468 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.65 % Allowed : 23.82 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.41), residues: 417 helix: 2.12 (0.35), residues: 211 sheet: -0.34 (0.71), residues: 62 loop : -0.97 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 263 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 0.002 0.000 ARG A 331 *********************** 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 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.367 Fit side-chains REVERT: A 272 ASP cc_start: 0.7575 (m-30) cc_final: 0.7274 (m-30) REVERT: A 286 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: A 335 ILE cc_start: 0.8487 (mt) cc_final: 0.8179 (mm) REVERT: A 376 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.7501 (mptp) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 1.3997 time to fit residues: 89.0930 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3408 Z= 0.221 Angle : 0.534 6.938 4628 Z= 0.276 Chirality : 0.043 0.128 502 Planarity : 0.005 0.049 592 Dihedral : 5.467 53.821 468 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.35 % Allowed : 23.82 % Favored : 73.82 % 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: 1.07 (0.41), residues: 417 helix: 2.15 (0.35), residues: 211 sheet: -0.38 (0.71), residues: 62 loop : -0.97 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 263 HIS 0.004 0.001 HIS A 388 PHE 0.012 0.002 PHE A 381 TYR 0.013 0.001 TYR A 363 ARG 0.002 0.000 ARG A 331 *********************** 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 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.387 Fit side-chains REVERT: A 218 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 272 ASP cc_start: 0.7598 (m-30) cc_final: 0.7301 (m-30) REVERT: A 286 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: A 335 ILE cc_start: 0.8444 (mt) cc_final: 0.8119 (mm) REVERT: A 376 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.7521 (mptp) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 1.4479 time to fit residues: 96.5368 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 193 GLN A 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3408 Z= 0.219 Angle : 0.537 7.310 4628 Z= 0.277 Chirality : 0.043 0.130 502 Planarity : 0.005 0.049 592 Dihedral : 5.413 54.110 468 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.06 % Allowed : 24.71 % Favored : 73.24 % 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: 1.10 (0.41), residues: 417 helix: 2.14 (0.35), residues: 211 sheet: -0.29 (0.72), residues: 62 loop : -0.94 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 263 HIS 0.004 0.001 HIS A 388 PHE 0.012 0.002 PHE A 381 TYR 0.013 0.001 TYR A 363 ARG 0.002 0.000 ARG A 331 *********************** 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 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.374 Fit side-chains REVERT: A 218 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 272 ASP cc_start: 0.7569 (m-30) cc_final: 0.7276 (m-30) REVERT: A 286 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: A 335 ILE cc_start: 0.8435 (mt) cc_final: 0.8102 (mm) REVERT: A 376 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.7561 (mptp) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 1.3700 time to fit residues: 88.6198 Evaluate side-chains 60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.0040 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3408 Z= 0.214 Angle : 0.535 7.355 4628 Z= 0.275 Chirality : 0.043 0.129 502 Planarity : 0.004 0.049 592 Dihedral : 5.418 54.769 468 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.76 % Allowed : 24.71 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.41), residues: 417 helix: 2.16 (0.35), residues: 211 sheet: -0.28 (0.72), residues: 62 loop : -0.95 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 263 HIS 0.004 0.001 HIS A 388 PHE 0.012 0.002 PHE A 381 TYR 0.012 0.001 TYR A 363 ARG 0.002 0.000 ARG A 331 ********************** 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 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.503 Fit side-chains REVERT: A 218 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 272 ASP cc_start: 0.7565 (m-30) cc_final: 0.7276 (m-30) REVERT: A 286 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: A 335 ILE cc_start: 0.8440 (mt) cc_final: 0.8109 (mm) REVERT: A 376 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.7564 (mptp) outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 1.5326 time to fit residues: 95.9094 Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.093182 restraints weight = 10674.490| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.21 r_work: 0.2718 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3408 Z= 0.288 Angle : 0.572 7.279 4628 Z= 0.298 Chirality : 0.045 0.132 502 Planarity : 0.005 0.049 592 Dihedral : 5.576 52.076 468 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.76 % Allowed : 25.00 % Favored : 73.24 % 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: 0.99 (0.41), residues: 417 helix: 2.09 (0.35), residues: 209 sheet: -0.28 (0.68), residues: 67 loop : -1.06 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 263 HIS 0.004 0.001 HIS A 388 PHE 0.015 0.002 PHE A 381 TYR 0.017 0.002 TYR A 363 ARG 0.002 0.000 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2057.26 seconds wall clock time: 37 minutes 33.53 seconds (2253.53 seconds total)