Starting phenix.real_space_refine on Mon Jan 13 20:54:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5w_19752/01_2025/8s5w_19752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5w_19752/01_2025/8s5w_19752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s5w_19752/01_2025/8s5w_19752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5w_19752/01_2025/8s5w_19752.map" model { file = "/net/cci-nas-00/data/ceres_data/8s5w_19752/01_2025/8s5w_19752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5w_19752/01_2025/8s5w_19752.cif" } resolution = 3.05 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= 0.001 sd= 0.053 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2662 2.51 5 N 626 2.21 5 O 700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4009 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 935 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3037 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 13, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'2TA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.58, per 1000 atoms: 0.89 Number of scatterers: 4009 At special positions: 0 Unit cell: (100.43, 79.68, 77.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 700 8.00 N 626 7.00 C 2662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 471.8 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 4 sheets defined 61.8% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 removed outlier: 3.651A pdb=" N THR A 16 " --> pdb=" O TRP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 56 through 66 removed outlier: 4.383A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.600A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 99 removed outlier: 4.204A pdb=" N VAL A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.622A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.745A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 163 removed outlier: 3.707A pdb=" N THR A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 187 removed outlier: 3.647A pdb=" N ASN A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 274 removed outlier: 3.655A pdb=" N SER A 274 " --> pdb=" O GLU A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 275 through 298 removed outlier: 3.539A pdb=" N TRP A 284 " --> pdb=" O TYR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 315 through 337 removed outlier: 3.601A pdb=" N GLY A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 366 removed outlier: 3.571A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 395 removed outlier: 3.671A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 426 removed outlier: 3.815A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 456 removed outlier: 4.016A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.605A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 7 " --> pdb=" O SER B 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.376A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLN B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET B 34 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.376A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLN B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET B 34 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 4.040A pdb=" N ARG B 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 592 1.27 - 1.41: 1172 1.41 - 1.54: 2297 1.54 - 1.68: 27 1.68 - 1.81: 36 Bond restraints: 4124 Sorted by residual: bond pdb=" CAR 2TA A 601 " pdb=" CAS 2TA A 601 " ideal model delta sigma weight residual 1.543 1.255 0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" CAO 2TA A 601 " pdb=" NAP 2TA A 601 " ideal model delta sigma weight residual 1.444 1.194 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" CAT 2TA A 601 " pdb=" NAP 2TA A 601 " ideal model delta sigma weight residual 1.456 1.279 0.177 2.00e-02 2.50e+03 7.79e+01 bond pdb=" C ARG A 277 " pdb=" O ARG A 277 " ideal model delta sigma weight residual 1.237 1.136 0.100 1.16e-02 7.43e+03 7.48e+01 bond pdb=" C2 2TA A 601 " pdb=" N1 2TA A 601 " ideal model delta sigma weight residual 1.322 1.482 -0.160 2.00e-02 2.50e+03 6.39e+01 ... (remaining 4119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 5578 3.46 - 6.93: 43 6.93 - 10.39: 2 10.39 - 13.86: 1 13.86 - 17.32: 2 Bond angle restraints: 5626 Sorted by residual: angle pdb=" N VAL A 77 " pdb=" CA VAL A 77 " pdb=" C VAL A 77 " ideal model delta sigma weight residual 110.05 101.20 8.85 1.09e+00 8.42e-01 6.59e+01 angle pdb=" OBJ 2TA A 601 " pdb=" SBD 2TA A 601 " pdb=" OBK 2TA A 601 " ideal model delta sigma weight residual 118.13 100.81 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" CA LEU A 190 " pdb=" C LEU A 190 " pdb=" N PRO A 191 " ideal model delta sigma weight residual 118.23 123.02 -4.79 9.20e-01 1.18e+00 2.72e+01 angle pdb=" C2 2TA A 601 " pdb=" NAF 2TA A 601 " pdb=" CAG 2TA A 601 " ideal model delta sigma weight residual 131.32 116.30 15.02 3.00e+00 1.11e-01 2.51e+01 angle pdb=" CA VAL A 77 " pdb=" C VAL A 77 " pdb=" O VAL A 77 " ideal model delta sigma weight residual 121.98 116.24 5.74 1.21e+00 6.83e-01 2.25e+01 ... (remaining 5621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.44: 2228 29.44 - 58.89: 103 58.89 - 88.33: 9 88.33 - 117.77: 3 117.77 - 147.22: 2 Dihedral angle restraints: 2345 sinusoidal: 873 harmonic: 1472 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 155.56 -62.56 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CAG 2TA A 601 " pdb=" C2 2TA A 601 " pdb=" NAF 2TA A 601 " pdb=" N1 2TA A 601 " ideal model delta sinusoidal sigma weight residual -0.72 -147.94 147.22 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" CAI 2TA A 601 " pdb=" CAJ 2TA A 601 " pdb=" OAM 2TA A 601 " pdb=" CAN 2TA A 601 " ideal model delta sinusoidal sigma weight residual -1.36 129.06 -130.42 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 2342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 499 0.048 - 0.096: 105 0.096 - 0.144: 22 0.144 - 0.192: 3 0.192 - 0.240: 1 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU A 190 " pdb=" N LEU A 190 " pdb=" C LEU A 190 " pdb=" CB LEU A 190 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA LYS B 87 " pdb=" N LYS B 87 " pdb=" C LYS B 87 " pdb=" CB LYS B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 627 not shown) Planarity restraints: 683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 80 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C LYS A 80 " -0.032 2.00e-02 2.50e+03 pdb=" O LYS A 80 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 81 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 190 " 0.007 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C LEU A 190 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 190 " 0.008 2.00e-02 2.50e+03 pdb=" N PRO A 191 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 13 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO B 14 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.017 5.00e-02 4.00e+02 ... (remaining 680 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1339 2.83 - 3.35: 3715 3.35 - 3.87: 6532 3.87 - 4.38: 8047 4.38 - 4.90: 13737 Nonbonded interactions: 33370 Sorted by model distance: nonbonded pdb=" O SER A 89 " pdb=" OG1 THR A 93 " model vdw 2.313 3.040 nonbonded pdb=" N VAL A 77 " pdb=" O VAL A 77 " model vdw 2.422 2.496 nonbonded pdb=" N ASN A 340 " pdb=" OD1 ASN A 340 " model vdw 2.428 3.120 nonbonded pdb=" O ASP B 73 " pdb=" OD1 ASP B 73 " model vdw 2.432 3.040 nonbonded pdb=" NAP 2TA A 601 " pdb=" OAM 2TA A 601 " model vdw 2.452 2.496 ... (remaining 33365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.190 Find NCS groups from input model: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.012 0.288 4124 Z= 0.808 Angle : 0.836 17.323 5626 Z= 0.478 Chirality : 0.043 0.240 630 Planarity : 0.004 0.030 683 Dihedral : 17.300 147.216 1406 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.24 % Allowed : 19.48 % Favored : 80.29 % 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: -1.89 (0.36), residues: 496 helix: -1.25 (0.29), residues: 275 sheet: -1.31 (0.86), residues: 43 loop : -0.91 (0.46), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 110 HIS 0.003 0.001 HIS A 200 PHE 0.007 0.001 PHE A 439 TYR 0.013 0.001 TYR A 336 ARG 0.003 0.001 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.404 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.2051 time to fit residues: 15.0324 Evaluate side-chains 58 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.153800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.137167 restraints weight = 4911.914| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.48 r_work: 0.3328 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4124 Z= 0.273 Angle : 0.615 6.583 5626 Z= 0.319 Chirality : 0.043 0.146 630 Planarity : 0.005 0.038 683 Dihedral : 11.603 153.736 571 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.51 % Allowed : 17.10 % Favored : 78.38 % 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: -0.32 (0.37), residues: 496 helix: 0.39 (0.30), residues: 293 sheet: -0.78 (0.83), residues: 45 loop : -0.99 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.013 0.002 PHE A 292 TYR 0.009 0.001 TYR A 336 ARG 0.007 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.452 Fit side-chains REVERT: B 52 SER cc_start: 0.8401 (m) cc_final: 0.8132 (t) REVERT: A 385 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8565 (tt) outliers start: 19 outliers final: 10 residues processed: 69 average time/residue: 0.1256 time to fit residues: 11.7951 Evaluate side-chains 69 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 452 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 0.0020 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.153639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.137030 restraints weight = 4900.167| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.49 r_work: 0.3340 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4124 Z= 0.242 Angle : 0.559 6.001 5626 Z= 0.289 Chirality : 0.041 0.148 630 Planarity : 0.004 0.040 683 Dihedral : 11.268 150.524 568 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.75 % Allowed : 18.76 % Favored : 76.48 % 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: 0.37 (0.38), residues: 496 helix: 1.01 (0.31), residues: 293 sheet: -0.43 (0.82), residues: 45 loop : -0.89 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.011 0.002 PHE A 439 TYR 0.013 0.001 TYR A 336 ARG 0.004 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.413 Fit side-chains REVERT: B 52 SER cc_start: 0.8334 (m) cc_final: 0.8091 (t) REVERT: A 385 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8636 (tt) outliers start: 20 outliers final: 13 residues processed: 71 average time/residue: 0.1227 time to fit residues: 11.8382 Evaluate side-chains 69 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.151451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.134640 restraints weight = 4919.422| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.53 r_work: 0.3297 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 4124 Z= 0.325 Angle : 0.604 6.041 5626 Z= 0.315 Chirality : 0.043 0.160 630 Planarity : 0.005 0.047 683 Dihedral : 11.542 150.986 568 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 6.41 % Allowed : 16.63 % Favored : 76.96 % 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: 0.34 (0.38), residues: 496 helix: 1.07 (0.31), residues: 293 sheet: -0.33 (0.79), residues: 45 loop : -1.14 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.003 0.001 HIS A 200 PHE 0.012 0.002 PHE A 439 TYR 0.011 0.001 TYR B 112 ARG 0.004 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.438 Fit side-chains REVERT: A 194 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7006 (mptt) REVERT: A 385 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8681 (tt) outliers start: 27 outliers final: 21 residues processed: 75 average time/residue: 0.1274 time to fit residues: 12.7346 Evaluate side-chains 80 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 452 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 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 = 0.151841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.135338 restraints weight = 5048.233| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.51 r_work: 0.3303 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 4124 Z= 0.318 Angle : 0.593 6.137 5626 Z= 0.309 Chirality : 0.043 0.159 630 Planarity : 0.005 0.049 683 Dihedral : 11.577 150.735 568 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.65 % Allowed : 16.63 % Favored : 76.72 % 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: 0.31 (0.38), residues: 496 helix: 1.11 (0.31), residues: 293 sheet: -0.47 (0.75), residues: 49 loop : -1.24 (0.45), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.002 PHE A 439 TYR 0.009 0.001 TYR B 112 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.433 Fit side-chains REVERT: B 100 SER cc_start: 0.6905 (OUTLIER) cc_final: 0.6606 (p) REVERT: A 194 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6908 (mptt) outliers start: 28 outliers final: 20 residues processed: 77 average time/residue: 0.1264 time to fit residues: 12.9322 Evaluate side-chains 77 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 452 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.0170 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.153306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.136684 restraints weight = 4978.650| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.51 r_work: 0.3330 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4124 Z= 0.223 Angle : 0.535 5.885 5626 Z= 0.279 Chirality : 0.041 0.148 630 Planarity : 0.005 0.049 683 Dihedral : 11.331 149.796 568 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.46 % Allowed : 18.76 % Favored : 75.77 % 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: 0.62 (0.38), residues: 496 helix: 1.38 (0.32), residues: 293 sheet: -0.37 (0.72), residues: 51 loop : -1.17 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.019 0.001 PHE A 439 TYR 0.007 0.001 TYR A 336 ARG 0.001 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.456 Fit side-chains REVERT: A 194 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6874 (mptt) outliers start: 23 outliers final: 20 residues processed: 72 average time/residue: 0.1289 time to fit residues: 12.3006 Evaluate side-chains 77 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN A 200 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.152881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.136433 restraints weight = 4974.560| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.47 r_work: 0.3316 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.004 0.051 4124 Z= 0.266 Angle : 0.557 5.933 5626 Z= 0.290 Chirality : 0.042 0.152 630 Planarity : 0.005 0.049 683 Dihedral : 11.433 149.999 568 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 6.41 % Allowed : 18.29 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.38), residues: 496 helix: 1.37 (0.31), residues: 293 sheet: -0.19 (0.74), residues: 49 loop : -1.25 (0.45), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.017 0.002 PHE A 439 TYR 0.010 0.001 TYR B 112 ARG 0.001 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 0.403 Fit side-chains REVERT: A 27 MET cc_start: 0.9116 (mmm) cc_final: 0.8876 (mmm) REVERT: A 194 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6810 (mptt) outliers start: 27 outliers final: 23 residues processed: 74 average time/residue: 0.1272 time to fit residues: 12.5463 Evaluate side-chains 77 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 0.0770 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.153834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.137681 restraints weight = 4946.057| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.45 r_work: 0.3331 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4124 Z= 0.249 Angle : 0.546 5.980 5626 Z= 0.285 Chirality : 0.042 0.151 630 Planarity : 0.005 0.048 683 Dihedral : 11.390 149.864 568 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 6.41 % Allowed : 18.76 % Favored : 74.82 % 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: 0.66 (0.38), residues: 496 helix: 1.44 (0.31), residues: 293 sheet: -0.32 (0.72), residues: 51 loop : -1.22 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.016 0.001 PHE A 439 TYR 0.009 0.001 TYR B 112 ARG 0.001 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 0.361 Fit side-chains REVERT: A 27 MET cc_start: 0.9112 (mmm) cc_final: 0.8878 (mmm) REVERT: A 194 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6779 (mptt) outliers start: 27 outliers final: 23 residues processed: 72 average time/residue: 0.1332 time to fit residues: 12.7648 Evaluate side-chains 75 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.153145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.137169 restraints weight = 4967.031| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.44 r_work: 0.3303 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 4124 Z= 0.326 Angle : 0.591 6.137 5626 Z= 0.308 Chirality : 0.044 0.159 630 Planarity : 0.005 0.049 683 Dihedral : 11.579 150.305 568 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 6.18 % Allowed : 19.00 % Favored : 74.82 % 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: 0.53 (0.38), residues: 496 helix: 1.31 (0.31), residues: 293 sheet: -0.18 (0.73), residues: 49 loop : -1.30 (0.45), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.017 0.002 PHE A 439 TYR 0.012 0.001 TYR B 112 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.454 Fit side-chains REVERT: A 27 MET cc_start: 0.9130 (mmm) cc_final: 0.8894 (mmm) REVERT: A 194 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6798 (tptt) outliers start: 26 outliers final: 24 residues processed: 70 average time/residue: 0.1216 time to fit residues: 11.4339 Evaluate side-chains 78 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.150554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.133961 restraints weight = 4970.792| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.50 r_work: 0.3293 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 4124 Z= 0.316 Angle : 0.588 6.235 5626 Z= 0.306 Chirality : 0.044 0.160 630 Planarity : 0.005 0.049 683 Dihedral : 11.572 149.932 568 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.18 % Allowed : 18.76 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.38), residues: 496 helix: 1.31 (0.31), residues: 293 sheet: -0.33 (0.71), residues: 56 loop : -1.29 (0.46), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.017 0.002 PHE A 439 TYR 0.012 0.001 TYR B 112 ARG 0.002 0.000 ARG A 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.400 Fit side-chains REVERT: A 27 MET cc_start: 0.9137 (mmm) cc_final: 0.8905 (mmm) REVERT: A 194 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6793 (tptt) REVERT: A 343 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5651 (tt) outliers start: 26 outliers final: 24 residues processed: 72 average time/residue: 0.1220 time to fit residues: 11.7526 Evaluate side-chains 81 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.0010 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.152204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.135715 restraints weight = 5002.305| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.50 r_work: 0.3322 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4124 Z= 0.254 Angle : 0.551 6.023 5626 Z= 0.287 Chirality : 0.042 0.154 630 Planarity : 0.005 0.049 683 Dihedral : 11.436 149.388 568 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.18 % Allowed : 19.24 % Favored : 74.58 % 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: 0.69 (0.38), residues: 496 helix: 1.46 (0.31), residues: 293 sheet: -0.33 (0.70), residues: 57 loop : -1.24 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.016 0.001 PHE A 439 TYR 0.011 0.001 TYR B 112 ARG 0.001 0.000 ARG B 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2380.33 seconds wall clock time: 43 minutes 4.14 seconds (2584.14 seconds total)