Starting phenix.real_space_refine on Thu Jul 18 19:59:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/07_2024/8znc_60267.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/07_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_60267/07_2024/8znc_60267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/07_2024/8znc_60267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/07_2024/8znc_60267.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/07_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 Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.61, per 1000 atoms: 1.37 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 0.38 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: 0.94 Time building geometry restraints manager: 1.55 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: 99.33 - 106.61: 115 106.61 - 113.88: 1905 113.88 - 121.15: 1671 121.15 - 128.43: 905 128.43 - 135.70: 32 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 2.520 nonbonded pdb=" OD1 ASP A 5 " pdb=" OG SER A 81 " model vdw 2.423 2.440 nonbonded pdb=" NE ARG A 73 " pdb=" OE1 GLU A 78 " model vdw 2.434 2.520 nonbonded pdb=" ND1 HIS A 388 " pdb=" O ILE A 393 " model vdw 2.446 2.520 nonbonded pdb=" NZ LYS A 69 " pdb=" OG1 THR A 175 " model vdw 2.506 2.520 ... (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: 1.400 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 17.210 Find NCS groups from input model: 0.040 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.490 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.380 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: 1.4045 time to fit residues: 102.3601 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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: 0.8733 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3408 Z= 0.215 Angle : 0.527 6.446 4628 Z= 0.277 Chirality : 0.044 0.130 502 Planarity : 0.004 0.046 592 Dihedral : 6.104 46.341 471 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.41 % Allowed : 22.65 % 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: 0.90 (0.42), residues: 417 helix: 1.95 (0.35), residues: 211 sheet: -0.60 (0.72), residues: 62 loop : -0.88 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 364 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 0.003 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 74 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.369 Fit side-chains REVERT: A 272 ASP cc_start: 0.7486 (m-30) cc_final: 0.7078 (m-30) REVERT: A 286 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: A 333 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7774 (mttt) REVERT: A 335 ILE cc_start: 0.8527 (mt) cc_final: 0.8209 (mm) REVERT: A 376 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.7483 (mptp) outliers start: 15 outliers final: 6 residues processed: 70 average time/residue: 1.4724 time to fit residues: 105.7473 Evaluate side-chains 63 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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: 0.8748 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3408 Z= 0.223 Angle : 0.535 8.577 4628 Z= 0.276 Chirality : 0.044 0.134 502 Planarity : 0.005 0.047 592 Dihedral : 5.418 46.076 468 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.94 % Allowed : 23.82 % 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: 0.97 (0.41), residues: 417 helix: 2.02 (0.35), residues: 211 sheet: -0.47 (0.71), residues: 62 loop : -0.90 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.005 0.001 HIS A 388 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 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 70 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.361 Fit side-chains REVERT: A 272 ASP cc_start: 0.7558 (m-30) cc_final: 0.7195 (m-30) REVERT: A 286 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: A 333 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7844 (mtpp) REVERT: A 335 ILE cc_start: 0.8544 (mt) cc_final: 0.8239 (mm) REVERT: A 376 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.7487 (mptp) outliers start: 10 outliers final: 4 residues processed: 68 average time/residue: 1.4118 time to fit residues: 98.3123 Evaluate side-chains 64 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- 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: 0.8740 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3408 Z= 0.195 Angle : 0.505 7.984 4628 Z= 0.262 Chirality : 0.043 0.129 502 Planarity : 0.004 0.048 592 Dihedral : 5.249 45.911 468 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 1.06 (0.41), residues: 417 helix: 2.11 (0.35), residues: 211 sheet: -0.41 (0.71), residues: 62 loop : -0.92 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 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 118 *********************** 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 65 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.380 Fit side-chains REVERT: A 272 ASP cc_start: 0.7430 (m-30) cc_final: 0.7184 (m-30) REVERT: A 286 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: A 333 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7768 (mttt) REVERT: A 335 ILE cc_start: 0.8516 (mt) cc_final: 0.8205 (mm) REVERT: A 376 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.7497 (mptp) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 1.4876 time to fit residues: 97.6449 Evaluate side-chains 64 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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: 10.0000 chunk 16 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3408 Z= 0.165 Angle : 0.491 7.344 4628 Z= 0.252 Chirality : 0.042 0.129 502 Planarity : 0.004 0.049 592 Dihedral : 5.105 47.007 468 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.65 % Allowed : 24.12 % 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: 1.20 (0.42), residues: 417 helix: 2.23 (0.35), residues: 211 sheet: -0.31 (0.72), residues: 62 loop : -0.89 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 263 HIS 0.003 0.001 HIS A 388 PHE 0.010 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 67 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.402 Fit side-chains REVERT: A 272 ASP cc_start: 0.7473 (m-30) cc_final: 0.7151 (m-30) REVERT: A 286 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: A 335 ILE cc_start: 0.8490 (mt) cc_final: 0.8189 (mm) REVERT: A 376 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.7569 (mptp) outliers start: 9 outliers final: 3 residues processed: 66 average time/residue: 1.4457 time to fit residues: 97.8456 Evaluate side-chains 60 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- 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: 0.8776 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3408 Z= 0.287 Angle : 0.551 7.237 4628 Z= 0.289 Chirality : 0.045 0.130 502 Planarity : 0.005 0.049 592 Dihedral : 5.448 43.789 468 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 0.97 (0.41), residues: 417 helix: 2.03 (0.35), residues: 210 sheet: -0.40 (0.71), residues: 62 loop : -0.95 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 263 HIS 0.006 0.001 HIS A 388 PHE 0.015 0.002 PHE A 381 TYR 0.017 0.002 TYR A 363 ARG 0.003 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 63 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.382 Fit side-chains REVERT: A 272 ASP cc_start: 0.7563 (m-30) cc_final: 0.7247 (m-30) REVERT: A 286 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: A 335 ILE cc_start: 0.8549 (mt) cc_final: 0.8222 (mm) REVERT: A 376 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.7472 (mptp) REVERT: A 383 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7621 (tt0) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 1.4701 time to fit residues: 93.4844 Evaluate side-chains 61 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 383 GLU 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: 0.8980 chunk 33 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 A 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3408 Z= 0.168 Angle : 0.502 9.609 4628 Z= 0.255 Chirality : 0.042 0.127 502 Planarity : 0.004 0.049 592 Dihedral : 5.153 46.666 468 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.76 % Allowed : 24.41 % 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: 1.16 (0.41), residues: 417 helix: 2.22 (0.35), residues: 211 sheet: -0.34 (0.71), residues: 62 loop : -0.92 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 263 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.011 0.001 TYR A 363 ARG 0.001 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 61 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.405 Fit side-chains REVERT: A 272 ASP cc_start: 0.7496 (m-30) cc_final: 0.7203 (m-30) REVERT: A 286 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: A 335 ILE cc_start: 0.8413 (mt) cc_final: 0.8085 (mm) REVERT: A 376 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.7544 (mptp) REVERT: A 383 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7587 (tt0) outliers start: 6 outliers final: 3 residues processed: 60 average time/residue: 1.5458 time to fit residues: 95.0425 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 383 GLU 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: 2.9990 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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: 0.8755 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3408 Z= 0.220 Angle : 0.525 8.554 4628 Z= 0.269 Chirality : 0.044 0.130 502 Planarity : 0.005 0.050 592 Dihedral : 5.299 45.075 468 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 1.09 (0.41), residues: 417 helix: 2.13 (0.35), residues: 211 sheet: -0.39 (0.71), residues: 62 loop : -0.88 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.005 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 118 *********************** 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 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.374 Fit side-chains REVERT: A 272 ASP cc_start: 0.7489 (m-30) cc_final: 0.7182 (m-30) REVERT: A 286 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: A 335 ILE cc_start: 0.8452 (mt) cc_final: 0.8120 (mm) REVERT: A 376 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.7519 (mptp) REVERT: A 383 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7586 (tt0) outliers start: 7 outliers final: 3 residues processed: 58 average time/residue: 1.4340 time to fit residues: 85.3042 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 383 GLU 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: 0.3980 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2370 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= 0.211 Angle : 0.522 8.059 4628 Z= 0.267 Chirality : 0.043 0.130 502 Planarity : 0.004 0.049 592 Dihedral : 5.238 45.636 468 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.06 % Allowed : 23.82 % Favored : 74.12 % 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: 2.15 (0.35), residues: 211 sheet: -0.35 (0.71), residues: 62 loop : -0.92 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 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 60 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.387 Fit side-chains REVERT: A 272 ASP cc_start: 0.7552 (m-30) cc_final: 0.7257 (m-30) REVERT: A 286 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: A 335 ILE cc_start: 0.8462 (mt) cc_final: 0.8141 (mm) REVERT: A 376 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.7515 (mptp) REVERT: A 383 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7591 (tt0) outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 1.4855 time to fit residues: 90.0989 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 383 GLU 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: 0.0570 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- 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: 0.8748 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3408 Z= 0.215 Angle : 0.523 7.799 4628 Z= 0.267 Chirality : 0.043 0.129 502 Planarity : 0.004 0.049 592 Dihedral : 5.253 45.685 468 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.76 % Allowed : 24.12 % Favored : 74.12 % 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: 1.09 (0.41), residues: 417 helix: 2.12 (0.35), residues: 212 sheet: -0.35 (0.71), residues: 62 loop : -0.91 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 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 fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.465 Fit side-chains REVERT: A 272 ASP cc_start: 0.7563 (m-30) cc_final: 0.7277 (m-30) REVERT: A 286 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: A 335 ILE cc_start: 0.8464 (mt) cc_final: 0.8140 (mm) REVERT: A 376 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.7518 (mptp) REVERT: A 383 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7591 (tt0) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 1.5160 time to fit residues: 90.2640 Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 383 GLU 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: 5.9990 chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.141969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.087160 restraints weight = 10754.286| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.54 r_work: 0.2701 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 3408 Z= 0.339 Angle : 0.590 7.823 4628 Z= 0.306 Chirality : 0.047 0.159 502 Planarity : 0.005 0.049 592 Dihedral : 5.528 42.983 468 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.76 % Allowed : 24.12 % Favored : 74.12 % 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: 0.86 (0.41), residues: 417 helix: 1.92 (0.35), residues: 211 sheet: -0.36 (0.72), residues: 61 loop : -1.04 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 263 HIS 0.005 0.001 HIS A 388 PHE 0.017 0.002 PHE A 381 TYR 0.019 0.002 TYR A 363 ARG 0.004 0.001 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.79 seconds wall clock time: 38 minutes 38.99 seconds (2318.99 seconds total)