Starting phenix.real_space_refine on Mon Jun 24 16:15:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/06_2024/8znc_60267_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/06_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_60267/06_2024/8znc_60267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/06_2024/8znc_60267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/06_2024/8znc_60267_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znc_60267/06_2024/8znc_60267_updated.pdb" } 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-5370/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: 4.24, per 1000 atoms: 1.26 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: 1.53 Conformation dependent library (CDL) restraints added in 1.2 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... running ksdssp... Secondary structure from input PDB file: 17 helices and 4 sheets defined 48.3% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.933A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 6.221A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.741A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 324 through 333 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) Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 366 through 390 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.636A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (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) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 removed outlier: 6.967A pdb=" N GLY A 106 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS A 75 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE A 108 " --> pdb=" O HIS A 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 3.730A pdb=" N ALA A 293 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 277 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.857A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 158 hydrogen bonds defined for protein. 463 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: 0.89 Time building geometry restraints manager: 1.67 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: 1298 2.91 - 3.40: 3435 3.40 - 3.90: 6201 3.90 - 4.40: 7024 4.40 - 4.90: 11154 Nonbonded interactions: 29112 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 29107 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.440 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.860 ------------------------------------------------------------------------------- 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= 0.438 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 : 0.371 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: 102.2552 Evaluate side-chains 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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: 6.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.8743 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3408 Z= 0.223 Angle : 0.528 6.265 4628 Z= 0.276 Chirality : 0.044 0.122 502 Planarity : 0.005 0.048 592 Dihedral : 6.121 46.028 471 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.41 % Allowed : 22.94 % 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: 0.91 (0.42), residues: 417 helix: 2.01 (0.36), residues: 208 sheet: -0.42 (0.69), residues: 67 loop : -0.98 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 364 HIS 0.004 0.001 HIS A 388 PHE 0.013 0.002 PHE A 381 TYR 0.014 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 76 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.377 Fit side-chains REVERT: A 272 ASP cc_start: 0.7515 (m-30) cc_final: 0.7161 (m-30) REVERT: A 333 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7775 (mttp) REVERT: A 335 ILE cc_start: 0.8544 (mt) cc_final: 0.8235 (mm) REVERT: A 376 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.7420 (mptp) outliers start: 15 outliers final: 6 residues processed: 72 average time/residue: 1.4304 time to fit residues: 105.5312 Evaluate side-chains 64 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 323 THR 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: 0.3980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.0970 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 overall best weight: 1.3580 ------------------------------------------------------------------------------- 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: 0.8722 moved from start: 0.1816 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= 0.166 Angle : 0.488 8.387 4628 Z= 0.250 Chirality : 0.042 0.125 502 Planarity : 0.004 0.049 592 Dihedral : 5.249 48.423 468 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.65 % Allowed : 24.71 % 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: 1.12 (0.42), residues: 417 helix: 2.14 (0.36), residues: 209 sheet: -0.27 (0.72), residues: 62 loop : -0.86 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.003 0.001 HIS A 388 PHE 0.011 0.001 PHE A 381 TYR 0.012 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 66 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.383 Fit side-chains REVERT: A 272 ASP cc_start: 0.7522 (m-30) cc_final: 0.7218 (m-30) REVERT: A 283 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7375 (mt-10) REVERT: A 333 LYS cc_start: 0.8214 (mtpt) cc_final: 0.8005 (mtpp) REVERT: A 335 ILE cc_start: 0.8519 (mt) cc_final: 0.8194 (mm) REVERT: A 376 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.7532 (mptp) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 1.4537 time to fit residues: 95.2938 Evaluate side-chains 64 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 323 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3408 Z= 0.208 Angle : 0.507 8.011 4628 Z= 0.262 Chirality : 0.043 0.133 502 Planarity : 0.005 0.049 592 Dihedral : 5.323 46.351 468 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.65 % Allowed : 24.71 % 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: 1.07 (0.42), residues: 417 helix: 2.06 (0.36), residues: 208 sheet: -0.11 (0.68), residues: 67 loop : -0.92 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.013 0.002 PHE A 381 TYR 0.014 0.001 TYR A 363 ARG 0.002 0.000 ARG A 165 *********************** 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: 9 poor density : 56 time to evaluate : 0.370 Fit side-chains REVERT: A 272 ASP cc_start: 0.7643 (m-30) cc_final: 0.7381 (m-30) REVERT: A 333 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7793 (mttt) REVERT: A 335 ILE cc_start: 0.8544 (mt) cc_final: 0.8220 (mm) REVERT: A 376 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.7488 (mptp) outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 1.4278 time to fit residues: 92.2254 Evaluate side-chains 62 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 323 THR 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=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: 0.8980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3408 Z= 0.145 Angle : 0.474 7.299 4628 Z= 0.241 Chirality : 0.041 0.134 502 Planarity : 0.004 0.049 592 Dihedral : 5.060 49.697 468 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.27 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: 1.32 (0.42), residues: 417 helix: 2.18 (0.36), residues: 210 sheet: -0.10 (0.72), residues: 62 loop : -0.61 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.000 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 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 61 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.380 Fit side-chains REVERT: A 272 ASP cc_start: 0.7623 (m-30) cc_final: 0.7339 (m-30) REVERT: A 335 ILE cc_start: 0.8457 (mt) cc_final: 0.8149 (mm) REVERT: A 376 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.7572 (mptp) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 1.4718 time to fit residues: 90.5047 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 323 THR 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: 0.9980 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 0.0000 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.0050 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- 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: 0.8710 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3408 Z= 0.149 Angle : 0.470 7.096 4628 Z= 0.239 Chirality : 0.041 0.131 502 Planarity : 0.004 0.049 592 Dihedral : 5.005 49.445 468 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.76 % Allowed : 25.29 % 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: 1.40 (0.42), residues: 417 helix: 2.23 (0.36), residues: 210 sheet: 0.01 (0.72), residues: 62 loop : -0.58 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.383 Fit side-chains REVERT: A 272 ASP cc_start: 0.7573 (m-30) cc_final: 0.7308 (m-30) REVERT: A 300 VAL cc_start: 0.8288 (m) cc_final: 0.8045 (p) REVERT: A 335 ILE cc_start: 0.8420 (mt) cc_final: 0.8081 (mm) REVERT: A 376 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.7565 (mptp) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 1.4338 time to fit residues: 85.3154 Evaluate side-chains 58 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 323 THR 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: 0.9980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.0870 chunk 25 optimal weight: 0.0270 overall best weight: 0.6216 ------------------------------------------------------------------------------- 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: 0.8675 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3408 Z= 0.134 Angle : 0.465 7.374 4628 Z= 0.233 Chirality : 0.041 0.131 502 Planarity : 0.004 0.049 592 Dihedral : 4.827 51.169 468 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.47 % Allowed : 25.59 % 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: 1.51 (0.42), residues: 417 helix: 2.30 (0.36), residues: 210 sheet: 0.12 (0.72), residues: 62 loop : -0.52 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.007 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: 5 poor density : 56 time to evaluate : 0.374 Fit side-chains REVERT: A 272 ASP cc_start: 0.7563 (m-30) cc_final: 0.7274 (m-30) REVERT: A 300 VAL cc_start: 0.8255 (m) cc_final: 0.8043 (p) REVERT: A 335 ILE cc_start: 0.8405 (mt) cc_final: 0.8091 (mm) outliers start: 5 outliers final: 3 residues processed: 59 average time/residue: 1.4244 time to fit residues: 86.1853 Evaluate side-chains 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.8704 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3408 Z= 0.155 Angle : 0.479 6.658 4628 Z= 0.242 Chirality : 0.041 0.128 502 Planarity : 0.004 0.049 592 Dihedral : 4.902 49.606 468 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.18 % Allowed : 26.47 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.42), residues: 417 helix: 2.26 (0.36), residues: 210 sheet: 0.09 (0.72), residues: 62 loop : -0.51 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.009 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 57 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 272 ASP cc_start: 0.7565 (m-30) cc_final: 0.7295 (m-30) REVERT: A 300 VAL cc_start: 0.8267 (m) cc_final: 0.8041 (p) REVERT: A 327 ASP cc_start: 0.7946 (m-30) cc_final: 0.7646 (m-30) REVERT: A 335 ILE cc_start: 0.8402 (mt) cc_final: 0.8083 (mm) REVERT: A 376 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.7572 (mptp) outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 1.5397 time to fit residues: 88.3511 Evaluate side-chains 56 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR 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: 4.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.8738 moved from start: 0.2251 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= 0.190 Angle : 0.505 6.626 4628 Z= 0.257 Chirality : 0.043 0.125 502 Planarity : 0.005 0.049 592 Dihedral : 5.092 47.184 468 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.47 % Allowed : 25.88 % 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: 1.40 (0.42), residues: 417 helix: 2.27 (0.36), residues: 209 sheet: 0.11 (0.69), residues: 67 loop : -0.71 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 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 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: 5 poor density : 55 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 272 ASP cc_start: 0.7577 (m-30) cc_final: 0.7318 (m-30) REVERT: A 300 VAL cc_start: 0.8278 (m) cc_final: 0.8016 (p) REVERT: A 327 ASP cc_start: 0.8051 (m-30) cc_final: 0.7718 (m-30) REVERT: A 335 ILE cc_start: 0.8391 (mt) cc_final: 0.8065 (mm) REVERT: A 376 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.7563 (mptp) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 1.6121 time to fit residues: 99.0830 Evaluate side-chains 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR 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: 9.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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: 0.8755 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3408 Z= 0.224 Angle : 0.524 6.709 4628 Z= 0.269 Chirality : 0.044 0.122 502 Planarity : 0.005 0.050 592 Dihedral : 5.274 45.939 468 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.76 % Allowed : 25.59 % 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: 1.29 (0.42), residues: 417 helix: 2.16 (0.36), residues: 209 sheet: 0.02 (0.69), residues: 67 loop : -0.71 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.014 0.002 PHE A 381 TYR 0.014 0.001 TYR A 363 ARG 0.006 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 fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.384 Fit side-chains REVERT: A 272 ASP cc_start: 0.7563 (m-30) cc_final: 0.7301 (m-30) REVERT: A 327 ASP cc_start: 0.8060 (m-30) cc_final: 0.7739 (m-30) REVERT: A 335 ILE cc_start: 0.8409 (mt) cc_final: 0.8077 (mm) REVERT: A 376 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.7510 (mptp) outliers start: 6 outliers final: 2 residues processed: 61 average time/residue: 1.5141 time to fit residues: 94.8830 Evaluate side-chains 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR 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: 0.7980 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.144307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.090928 restraints weight = 10788.819| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.60 r_work: 0.2760 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2319 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= 0.208 Angle : 0.515 6.699 4628 Z= 0.263 Chirality : 0.043 0.124 502 Planarity : 0.005 0.050 592 Dihedral : 5.226 46.622 468 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.88 % Allowed : 26.76 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.42), residues: 417 helix: 2.16 (0.36), residues: 209 sheet: -0.03 (0.68), residues: 67 loop : -0.78 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.013 0.002 PHE A 381 TYR 0.013 0.001 TYR A 363 ARG 0.005 0.000 ARG A 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2093.61 seconds wall clock time: 37 minutes 22.32 seconds (2242.32 seconds total)