Starting phenix.real_space_refine on Wed Mar 5 17:34:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrp_18622/03_2025/8qrp_18622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrp_18622/03_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_18622/03_2025/8qrp_18622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrp_18622/03_2025/8qrp_18622.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrp_18622/03_2025/8qrp_18622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrp_18622/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.64, per 1000 atoms: 0.85 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: 0.75 Conformation dependent library (CDL) restraints added in 456.9 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: 0.30 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: 0.88 Time building geometry restraints manager: 0.84 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.250 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- 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 : 0.344 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 1.1129 time to fit residues: 49.4676 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 : 0.338 ------------------------------------------------------------------------------- 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: 0.5980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.142102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107952 restraints weight = 3702.550| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.86 r_work: 0.3251 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3175 Z= 0.274 Angle : 0.541 5.223 4324 Z= 0.280 Chirality : 0.039 0.139 542 Planarity : 0.005 0.042 535 Dihedral : 3.407 13.634 440 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.26 % Allowed : 14.29 % Favored : 81.46 % 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: 1.93 (0.41), residues: 413 helix: 1.92 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.32 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 275 HIS 0.001 0.001 HIS B 313 PHE 0.013 0.002 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: 14 poor density : 47 time to evaluate : 0.365 Fit side-chains REVERT: B 251 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: B 253 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7628 (mm-30) REVERT: B 331 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7754 (mtmm) REVERT: B 387 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8696 (mmm) REVERT: B 475 ASP cc_start: 0.7672 (m-30) cc_final: 0.7396 (m-30) outliers start: 14 outliers final: 6 residues processed: 54 average time/residue: 1.0752 time to fit residues: 59.9964 Evaluate side-chains 51 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 VAL 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 387 MET 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: 0.7980 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 30 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 = 0.3741 r_free = 0.3741 target = 0.145000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111211 restraints weight = 3635.680| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.79 r_work: 0.3280 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1726 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= 0.194 Angle : 0.475 5.003 4324 Z= 0.244 Chirality : 0.038 0.138 542 Planarity : 0.004 0.040 535 Dihedral : 3.302 13.805 440 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 : 14.29 % Favored : 82.07 % 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: 2.30 (0.42), residues: 413 helix: 2.06 (0.28), residues: 332 sheet: -0.51 (1.19), residues: 20 loop : -0.72 (0.82), residues: 61 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 0.010 0.001 PHE B 237 TYR 0.009 0.002 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 62 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.311 Fit side-chains REVERT: B 251 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: B 253 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7618 (mm-30) REVERT: B 366 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7806 (mt-10) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 1.0418 time to fit residues: 59.2433 Evaluate side-chains 52 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.0470 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 0.0060 chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4294 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.147420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113728 restraints weight = 3648.681| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.78 r_work: 0.3331 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3175 Z= 0.148 Angle : 0.448 4.893 4324 Z= 0.230 Chirality : 0.037 0.132 542 Planarity : 0.004 0.040 535 Dihedral : 3.179 15.070 440 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 : 16.11 % 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: 2.66 (0.41), residues: 413 helix: 2.23 (0.28), residues: 337 sheet: -0.72 (1.17), residues: 20 loop : -0.15 (0.81), residues: 56 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 0.011 0.001 PHE B 393 TYR 0.008 0.001 TYR B 208 ARG 0.002 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 67 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.345 Fit side-chains REVERT: B 251 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: B 253 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7579 (mm-30) REVERT: B 475 ASP cc_start: 0.7517 (m-30) cc_final: 0.7222 (m-30) outliers start: 11 outliers final: 4 residues processed: 60 average time/residue: 0.9037 time to fit residues: 56.2986 Evaluate side-chains 53 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 251 GLU 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: 0.5980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.144705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110576 restraints weight = 3659.922| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.79 r_work: 0.3252 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3175 Z= 0.204 Angle : 0.473 5.021 4324 Z= 0.241 Chirality : 0.038 0.139 542 Planarity : 0.004 0.039 535 Dihedral : 3.226 14.008 440 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.95 % Allowed : 15.81 % 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: 2.53 (0.42), residues: 413 helix: 2.25 (0.28), residues: 333 sheet: -0.46 (1.17), residues: 21 loop : -0.86 (0.77), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 338 HIS 0.000 0.000 HIS B 313 PHE 0.011 0.001 PHE B 237 TYR 0.010 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 59 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.311 Fit side-chains REVERT: B 251 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: B 331 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7712 (mtmm) outliers start: 13 outliers final: 7 residues processed: 52 average time/residue: 0.9946 time to fit residues: 53.5671 Evaluate side-chains 54 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.145024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110911 restraints weight = 3774.113| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.82 r_work: 0.3253 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2093 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= 0.179 Angle : 0.465 5.006 4324 Z= 0.236 Chirality : 0.037 0.139 542 Planarity : 0.004 0.039 535 Dihedral : 3.193 14.602 440 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 : 16.11 % 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: 2.71 (0.41), residues: 413 helix: 2.31 (0.28), residues: 337 sheet: -0.59 (1.17), residues: 21 loop : -0.46 (0.76), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 338 HIS 0.001 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 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: 11 poor density : 47 time to evaluate : 0.342 Fit side-chains REVERT: B 251 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: B 331 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7729 (mtmm) REVERT: B 366 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7902 (mt-10) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 0.9569 time to fit residues: 50.7072 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 LYS 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: 0.7980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.145466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111643 restraints weight = 3674.727| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.79 r_work: 0.3261 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2160 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= 0.167 Angle : 0.454 4.930 4324 Z= 0.231 Chirality : 0.037 0.137 542 Planarity : 0.004 0.038 535 Dihedral : 3.164 14.612 440 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.95 % Allowed : 15.81 % 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: 2.80 (0.41), residues: 413 helix: 2.41 (0.28), residues: 336 sheet: -0.64 (1.17), residues: 21 loop : -0.65 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 338 HIS 0.000 0.000 HIS B 313 PHE 0.010 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 59 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.357 Fit side-chains REVERT: B 251 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: B 366 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7883 (mt-10) REVERT: B 475 ASP cc_start: 0.7639 (m-30) cc_final: 0.7388 (m-30) outliers start: 13 outliers final: 9 residues processed: 51 average time/residue: 1.0271 time to fit residues: 54.2365 Evaluate side-chains 54 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.143926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110019 restraints weight = 3705.883| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.78 r_work: 0.3234 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3175 Z= 0.208 Angle : 0.475 5.013 4324 Z= 0.241 Chirality : 0.038 0.139 542 Planarity : 0.004 0.039 535 Dihedral : 3.225 14.528 440 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.65 % Allowed : 15.81 % 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: 2.73 (0.41), residues: 413 helix: 2.36 (0.28), residues: 336 sheet: -0.68 (1.17), residues: 21 loop : -0.64 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.010 0.002 TYR B 334 ARG 0.001 0.000 ARG B 101 *********************** 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 55 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.323 Fit side-chains REVERT: B 251 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7473 (mp0) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 1.0166 time to fit residues: 50.5550 Evaluate side-chains 52 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 LYS 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: 0.6980 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.145046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111205 restraints weight = 3692.091| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.78 r_work: 0.3248 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2194 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= 0.179 Angle : 0.465 4.907 4324 Z= 0.236 Chirality : 0.037 0.138 542 Planarity : 0.004 0.038 535 Dihedral : 3.200 14.651 440 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.34 % Allowed : 16.72 % 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: 2.78 (0.41), residues: 413 helix: 2.40 (0.28), residues: 336 sheet: -0.74 (1.18), residues: 21 loop : -0.64 (0.72), 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 316 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 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 57 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.325 Fit side-chains REVERT: B 251 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7422 (mp0) outliers start: 11 outliers final: 9 residues processed: 50 average time/residue: 0.9261 time to fit residues: 48.0482 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 : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 LYS 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: 2.9990 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.144263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110012 restraints weight = 3666.630| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.83 r_work: 0.3247 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3175 Z= 0.212 Angle : 0.482 4.983 4324 Z= 0.244 Chirality : 0.038 0.141 542 Planarity : 0.004 0.038 535 Dihedral : 3.251 14.321 440 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.34 % Allowed : 16.72 % 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: 2.72 (0.41), residues: 413 helix: 2.36 (0.28), residues: 336 sheet: -0.82 (1.18), residues: 21 loop : -0.63 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 338 HIS 0.001 0.000 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.010 0.002 TYR B 334 ARG 0.001 0.000 ARG B 189 ********************** 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 54 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.282 Fit side-chains REVERT: B 251 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7477 (mp0) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 1.0078 time to fit residues: 49.0268 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 : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 LYS 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: 0.7980 chunk 26 optimal weight: 0.0470 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.146729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112966 restraints weight = 3677.114| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.82 r_work: 0.3279 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3175 Z= 0.151 Angle : 0.453 5.003 4324 Z= 0.229 Chirality : 0.037 0.136 542 Planarity : 0.004 0.038 535 Dihedral : 3.155 15.502 440 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.34 % Allowed : 16.72 % 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: 2.95 (0.41), residues: 413 helix: 2.53 (0.28), residues: 336 sheet: -0.79 (1.18), residues: 21 loop : -0.62 (0.72), 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 316 PHE 0.009 0.001 PHE B 237 TYR 0.008 0.001 TYR B 208 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: 2592.08 seconds wall clock time: 45 minutes 2.66 seconds (2702.66 seconds total)