Starting phenix.real_space_refine on Mon Feb 10 22:36:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrp_18622/02_2025/8qrp_18622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrp_18622/02_2025/8qrp_18622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrp_18622/02_2025/8qrp_18622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrp_18622/02_2025/8qrp_18622.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrp_18622/02_2025/8qrp_18622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrp_18622/02_2025/8qrp_18622.cif" } resolution = 2.7 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= 1.000 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 S 15 5.16 5 Na 3 4.78 5 C 2049 2.51 5 N 511 2.21 5 O 545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3123 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3110 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 16, 'TRANS': 402} Chain breaks: 2 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' NA': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 2.58, per 1000 atoms: 0.83 Number of scatterers: 3123 At special positions: 0 Unit cell: (62.7, 71.896, 74.404, 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 15 16.00 Na 3 11.00 O 545 8.00 N 511 7.00 C 2049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 412.5 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 86.7% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 76 through 82 removed outlier: 3.565A pdb=" N ALA B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 103 removed outlier: 4.283A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.684A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.723A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 292 removed outlier: 3.802A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.506A pdb=" N LYS B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.556A pdb=" N ARG B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 319 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.592A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 removed outlier: 3.596A pdb=" N THR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 386 Proline residue: B 380 - end of helix removed outlier: 3.987A pdb=" N THR B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 428 Processing helix chain 'B' and resid 438 through 447 removed outlier: 3.671A pdb=" N ILE B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.867A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TRP B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 210 257 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 989 1.34 - 1.46: 519 1.46 - 1.57: 1643 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3175 Sorted by residual: bond pdb=" CB MET B 274 " pdb=" CG MET B 274 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 5.02e-01 bond pdb=" CA ARG B 330 " pdb=" C ARG B 330 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 4.92e-01 bond pdb=" C PHE B 91 " pdb=" N PRO B 92 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.28e-02 6.10e+03 3.40e-01 bond pdb=" C VAL B 472 " pdb=" O VAL B 472 " ideal model delta sigma weight residual 1.240 1.233 0.007 1.18e-02 7.18e+03 3.08e-01 bond pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " ideal model delta sigma weight residual 1.537 1.544 -0.007 1.30e-02 5.92e+03 2.84e-01 ... (remaining 3170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 4225 1.24 - 2.49: 76 2.49 - 3.73: 15 3.73 - 4.98: 6 4.98 - 6.22: 2 Bond angle restraints: 4324 Sorted by residual: angle pdb=" C VAL B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta sigma weight residual 119.98 121.98 -2.00 1.11e+00 8.12e-01 3.26e+00 angle pdb=" CA LEU B 297 " pdb=" CB LEU B 297 " pdb=" CG LEU B 297 " ideal model delta sigma weight residual 116.30 122.52 -6.22 3.50e+00 8.16e-02 3.16e+00 angle pdb=" N PHE B 299 " pdb=" CA PHE B 299 " pdb=" C PHE B 299 " ideal model delta sigma weight residual 113.20 111.08 2.12 1.21e+00 6.83e-01 3.08e+00 angle pdb=" C VAL B 459 " pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " ideal model delta sigma weight residual 111.85 109.86 1.99 1.27e+00 6.20e-01 2.45e+00 angle pdb=" C LEU B 70 " pdb=" N GLY B 71 " pdb=" CA GLY B 71 " ideal model delta sigma weight residual 119.94 121.57 -1.63 1.11e+00 8.12e-01 2.16e+00 ... (remaining 4319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.76: 1593 13.76 - 27.51: 202 27.51 - 41.26: 50 41.26 - 55.02: 15 55.02 - 68.77: 3 Dihedral angle restraints: 1863 sinusoidal: 680 harmonic: 1183 Sorted by residual: dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual -180.00 -121.99 -58.01 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LYS B 219 " pdb=" CA LYS B 219 " pdb=" CB LYS B 219 " pdb=" CG LYS B 219 " ideal model delta sinusoidal sigma weight residual -60.00 -112.41 52.41 3 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" CA ILE B 231 " pdb=" CB ILE B 231 " pdb=" CG1 ILE B 231 " pdb=" CD1 ILE B 231 " ideal model delta sinusoidal sigma weight residual 180.00 127.88 52.12 3 1.50e+01 4.44e-03 9.08e+00 ... (remaining 1860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 365 0.027 - 0.053: 98 0.053 - 0.080: 57 0.080 - 0.107: 18 0.107 - 0.133: 4 Chirality restraints: 542 Sorted by residual: chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL B 220 " pdb=" N VAL B 220 " pdb=" C VAL B 220 " pdb=" CB VAL B 220 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA THR B 342 " pdb=" N THR B 342 " pdb=" C THR B 342 " pdb=" CB THR B 342 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.11 2.00e-01 2.50e+01 3.03e-01 ... (remaining 539 not shown) Planarity restraints: 535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 357 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO B 358 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 120 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 121 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 91 " -0.016 5.00e-02 4.00e+02 2.35e-02 8.85e-01 pdb=" N PRO B 92 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 92 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 92 " -0.013 5.00e-02 4.00e+02 ... (remaining 532 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 856 2.81 - 3.33: 3193 3.33 - 3.85: 5339 3.85 - 4.38: 6178 4.38 - 4.90: 10860 Nonbonded interactions: 26426 Sorted by model distance: nonbonded pdb=" OG1 THR B 139 " pdb="NA NA B 603 " model vdw 2.285 2.470 nonbonded pdb=" OD1 ASN B 386 " pdb="NA NA B 603 " model vdw 2.292 2.470 nonbonded pdb=" OD1 ASP B 388 " pdb="NA NA B 603 " model vdw 2.303 2.470 nonbonded pdb=" OG SER B 353 " pdb=" OXT GLN B 604 " model vdw 2.304 3.040 nonbonded pdb=" O PHE B 135 " pdb="NA NA B 603 " model vdw 2.315 2.470 ... (remaining 26421 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=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: 0.570 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.410 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.002 0.025 3175 Z= 0.143 Angle : 0.474 6.222 4324 Z= 0.262 Chirality : 0.035 0.133 542 Planarity : 0.004 0.044 535 Dihedral : 13.506 68.775 1103 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 16.41 % Favored : 83.59 % 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: 1.62 (0.41), residues: 413 helix: 1.58 (0.28), residues: 325 sheet: 0.09 (1.38), residues: 20 loop : -0.97 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 130 HIS 0.001 0.000 HIS B 373 PHE 0.012 0.001 PHE B 393 TYR 0.007 0.001 TYR B 208 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 1.1424 time to fit residues: 50.7314 Evaluate side-chains 41 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.143532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110072 restraints weight = 3694.237| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.79 r_work: 0.3274 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3175 Z= 0.214 Angle : 0.514 5.075 4324 Z= 0.264 Chirality : 0.038 0.141 542 Planarity : 0.005 0.041 535 Dihedral : 3.382 14.926 440 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.65 % Allowed : 13.98 % Favored : 82.37 % 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: 2.05 (0.42), residues: 413 helix: 1.98 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.23 (0.65), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 275 HIS 0.001 0.000 HIS B 313 PHE 0.012 0.001 PHE B 237 TYR 0.010 0.002 TYR B 276 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.437 Fit side-chains REVERT: B 251 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: B 253 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7591 (mm-30) REVERT: B 475 ASP cc_start: 0.7713 (m-30) cc_final: 0.7435 (m-30) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 1.1436 time to fit residues: 64.8448 Evaluate side-chains 49 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.0770 chunk 37 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112086 restraints weight = 3628.687| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.85 r_work: 0.3288 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3175 Z= 0.172 Angle : 0.462 4.938 4324 Z= 0.238 Chirality : 0.037 0.135 542 Planarity : 0.004 0.040 535 Dihedral : 3.223 14.667 440 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.34 % Allowed : 15.50 % Favored : 81.16 % 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: 2.44 (0.42), residues: 413 helix: 2.18 (0.28), residues: 332 sheet: -0.49 (1.20), residues: 20 loop : -0.77 (0.81), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 338 HIS 0.001 0.000 HIS B 313 PHE 0.009 0.001 PHE B 237 TYR 0.008 0.001 TYR B 208 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.319 Fit side-chains REVERT: B 251 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: B 253 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7569 (mm-30) REVERT: B 291 GLU cc_start: 0.7931 (pt0) cc_final: 0.7723 (pt0) REVERT: B 331 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7759 (mtmm) REVERT: B 366 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7832 (mt-10) outliers start: 11 outliers final: 3 residues processed: 57 average time/residue: 1.0185 time to fit residues: 60.1180 Evaluate side-chains 52 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111391 restraints weight = 3660.025| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.80 r_work: 0.3254 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3175 Z= 0.193 Angle : 0.470 4.989 4324 Z= 0.242 Chirality : 0.038 0.140 542 Planarity : 0.004 0.039 535 Dihedral : 3.226 13.980 440 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.86 % Allowed : 14.29 % Favored : 80.85 % 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: 2.53 (0.42), residues: 413 helix: 2.24 (0.28), residues: 333 sheet: -0.76 (1.15), residues: 20 loop : -0.66 (0.80), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 338 HIS 0.001 0.000 HIS B 373 PHE 0.011 0.001 PHE B 237 TYR 0.009 0.002 TYR B 334 ARG 0.001 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.354 Fit side-chains REVERT: B 251 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: B 331 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7787 (mtmm) outliers start: 16 outliers final: 6 residues processed: 55 average time/residue: 1.0523 time to fit residues: 59.8783 Evaluate side-chains 53 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 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 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110655 restraints weight = 3665.667| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.78 r_work: 0.3241 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3175 Z= 0.199 Angle : 0.471 5.000 4324 Z= 0.240 Chirality : 0.038 0.138 542 Planarity : 0.004 0.039 535 Dihedral : 3.237 14.169 440 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.95 % Allowed : 16.11 % Favored : 79.94 % 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: 2.53 (0.41), residues: 413 helix: 2.25 (0.28), residues: 333 sheet: -0.53 (1.16), residues: 21 loop : -0.89 (0.77), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 338 HIS 0.001 0.000 HIS B 373 PHE 0.011 0.001 PHE B 237 TYR 0.009 0.002 TYR B 334 ARG 0.001 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.314 Fit side-chains REVERT: B 251 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: B 331 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7734 (mtmm) outliers start: 13 outliers final: 7 residues processed: 54 average time/residue: 0.9391 time to fit residues: 52.5876 Evaluate side-chains 56 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110445 restraints weight = 3780.584| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.82 r_work: 0.3230 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3175 Z= 0.192 Angle : 0.470 5.038 4324 Z= 0.239 Chirality : 0.038 0.139 542 Planarity : 0.004 0.038 535 Dihedral : 3.225 14.380 440 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.65 % Allowed : 16.11 % Favored : 80.24 % 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: 2.68 (0.41), residues: 413 helix: 2.30 (0.28), residues: 336 sheet: -0.61 (1.16), residues: 21 loop : -0.50 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 338 HIS 0.000 0.000 HIS B 373 PHE 0.010 0.001 PHE B 237 TYR 0.009 0.002 TYR B 334 ARG 0.001 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.321 Fit side-chains REVERT: B 251 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: B 331 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7690 (mtmm) REVERT: B 366 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7860 (mt-10) outliers start: 12 outliers final: 8 residues processed: 52 average time/residue: 1.0050 time to fit residues: 54.1650 Evaluate side-chains 56 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111827 restraints weight = 3683.458| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.78 r_work: 0.3253 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3175 Z= 0.165 Angle : 0.454 4.922 4324 Z= 0.231 Chirality : 0.037 0.137 542 Planarity : 0.004 0.038 535 Dihedral : 3.181 15.158 440 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.04 % Allowed : 16.41 % Favored : 80.55 % 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: 2.83 (0.41), residues: 413 helix: 2.42 (0.28), residues: 336 sheet: -0.64 (1.18), residues: 21 loop : -0.58 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 338 HIS 0.000 0.000 HIS B 313 PHE 0.009 0.001 PHE B 237 TYR 0.008 0.001 TYR B 208 ARG 0.001 0.000 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.311 Fit side-chains REVERT: B 194 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8635 (p) REVERT: B 251 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: B 366 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7852 (mt-10) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 1.0169 time to fit residues: 54.7950 Evaluate side-chains 54 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111610 restraints weight = 3703.380| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.79 r_work: 0.3246 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.003 0.030 3175 Z= 0.177 Angle : 0.459 4.947 4324 Z= 0.234 Chirality : 0.037 0.139 542 Planarity : 0.004 0.038 535 Dihedral : 3.191 15.024 440 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.34 % Allowed : 16.41 % Favored : 80.24 % 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: 2.87 (0.41), residues: 413 helix: 2.45 (0.28), residues: 336 sheet: -0.68 (1.18), residues: 21 loop : -0.59 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 338 HIS 0.000 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.008 0.001 TYR B 334 ARG 0.001 0.000 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.352 Fit side-chains REVERT: B 194 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8645 (p) REVERT: B 251 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: B 366 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7870 (mt-10) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 1.0150 time to fit residues: 53.5599 Evaluate side-chains 55 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111308 restraints weight = 3697.050| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.75 r_work: 0.3245 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3175 Z= 0.188 Angle : 0.466 4.962 4324 Z= 0.237 Chirality : 0.038 0.139 542 Planarity : 0.004 0.038 535 Dihedral : 3.212 14.739 440 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.65 % Allowed : 16.41 % Favored : 79.94 % 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: 2.84 (0.41), residues: 413 helix: 2.44 (0.28), residues: 336 sheet: -0.77 (1.17), residues: 21 loop : -0.56 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 338 HIS 0.000 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.009 0.002 TYR B 334 ARG 0.001 0.000 ARG B 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.343 Fit side-chains REVERT: B 251 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7460 (mp0) outliers start: 12 outliers final: 9 residues processed: 50 average time/residue: 1.0719 time to fit residues: 55.4471 Evaluate side-chains 53 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111358 restraints weight = 3668.478| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.80 r_work: 0.3247 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3175 Z= 0.183 Angle : 0.467 4.959 4324 Z= 0.237 Chirality : 0.038 0.139 542 Planarity : 0.004 0.038 535 Dihedral : 3.216 14.836 440 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.34 % Allowed : 17.33 % Favored : 79.33 % 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: 2.88 (0.41), residues: 413 helix: 2.47 (0.28), residues: 336 sheet: -0.83 (1.18), residues: 21 loop : -0.57 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 338 HIS 0.000 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.009 0.002 TYR B 334 ARG 0.001 0.000 ARG B 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.347 Fit side-chains REVERT: B 251 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7463 (mp0) outliers start: 11 outliers final: 9 residues processed: 50 average time/residue: 1.0297 time to fit residues: 53.2960 Evaluate side-chains 55 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111784 restraints weight = 3679.572| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.80 r_work: 0.3250 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3175 Z= 0.174 Angle : 0.464 5.099 4324 Z= 0.235 Chirality : 0.037 0.138 542 Planarity : 0.004 0.038 535 Dihedral : 3.202 15.107 440 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.34 % Allowed : 17.33 % Favored : 79.33 % 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: 2.92 (0.41), residues: 413 helix: 2.50 (0.28), residues: 336 sheet: -0.88 (1.18), residues: 21 loop : -0.56 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 338 HIS 0.000 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 TYR 0.008 0.001 TYR B 334 ARG 0.001 0.000 ARG B 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2594.34 seconds wall clock time: 46 minutes 23.06 seconds (2783.06 seconds total)