Starting phenix.real_space_refine on Wed Jul 1 21:43:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrp_18622/07_2026/8qrp_18622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrp_18622/07_2026/8qrp_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qrp_18622/07_2026/8qrp_18622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrp_18622/07_2026/8qrp_18622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qrp_18622/07_2026/8qrp_18622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrp_18622/07_2026/8qrp_18622.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 10 Ad-hoc single atom residues: {' NA': 3} Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain breaks: 3 Time building chain proxies: 0.70, per 1000 atoms: 0.22 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: 0.26 Conformation dependent library (CDL) restraints added in 80.2 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: 0.05 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: 0.30 Time building geometry restraints manager: 0.33 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 3.210 nonbonded pdb=" OD1 ASN B 386 " pdb="NA NA B 603 " model vdw 2.292 3.210 nonbonded pdb=" OD1 ASP B 388 " pdb="NA NA B 603 " model vdw 2.303 3.210 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 3.210 ... (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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 3.460 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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= 0.106 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG B 301 TYR 0.007 0.001 TYR B 208 PHE 0.012 0.001 PHE B 393 TRP 0.007 0.001 TRP B 130 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 3175) covalent geometry : angle 0.47361 / 0.26 ( 4324) hydrogen bonds : bond 0.20658 / 14.81 ( 257) hydrogen bonds : angle 7.07678 / 5.43 ( 771) *********************** 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 : 0.117 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.3534 time to fit residues: 15.6979 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 : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.146017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112563 restraints weight = 3738.993| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.80 r_work: 0.3269 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3175 Z= 0.128 Angle : 0.501 4.992 4324 Z= 0.259 Chirality : 0.038 0.136 542 Planarity : 0.005 0.043 535 Dihedral : 3.356 17.093 440 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.65 % Allowed : 14.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.42), residues: 413 helix: 1.99 (0.29), residues: 334 sheet: -0.31 (1.28), residues: 20 loop : -0.59 (0.82), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.008 0.001 TYR B 276 PHE 0.010 0.001 PHE B 237 TRP 0.008 0.001 TRP B 338 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 3175) covalent geometry : angle 0.50053 / 0.26 ( 4324) hydrogen bonds : bond 0.04638 / 3.27 ( 257) hydrogen bonds : angle 4.84004 / 3.63 ( 771) *********************** 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 63 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.123 Fit side-chains REVERT: B 251 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: B 253 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7625 (mm-30) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 0.3207 time to fit residues: 18.8942 Evaluate side-chains 51 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.069 ------------------------------------------------------------------------------- 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 384 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 457 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.145449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108859 restraints weight = 3709.211| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.91 r_work: 0.3240 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1745 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= 0.140 Angle : 0.482 5.053 4324 Z= 0.249 Chirality : 0.038 0.141 542 Planarity : 0.004 0.040 535 Dihedral : 3.258 15.744 440 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.42), residues: 413 helix: 2.10 (0.28), residues: 334 sheet: -0.43 (1.20), residues: 20 loop : -0.60 (0.84), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.009 0.002 TYR B 208 PHE 0.011 0.001 PHE B 237 TRP 0.011 0.001 TRP B 338 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 3175) covalent geometry : angle 0.48196 / 0.25 ( 4324) hydrogen bonds : bond 0.04420 / 3.11 ( 257) hydrogen bonds : angle 4.63744 / 3.49 ( 771) *********************** 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 65 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.112 Fit side-chains REVERT: B 251 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: B 253 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7607 (mm-30) REVERT: B 366 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7814 (mt-10) outliers start: 14 outliers final: 5 residues processed: 59 average time/residue: 0.3731 time to fit residues: 22.7591 Evaluate side-chains 53 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.068 ------------------------------------------------------------------------------- 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 438 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3757 r_free = 0.3757 target = 0.146209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109692 restraints weight = 3679.387| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.90 r_work: 0.3300 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1953 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= 0.129 Angle : 0.468 4.944 4324 Z= 0.242 Chirality : 0.037 0.139 542 Planarity : 0.004 0.039 535 Dihedral : 3.204 15.741 440 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.56 % Allowed : 14.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.42), residues: 413 helix: 2.19 (0.28), residues: 335 sheet: -0.66 (1.18), residues: 20 loop : -0.58 (0.81), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.009 0.002 TYR B 208 PHE 0.011 0.001 PHE B 393 TRP 0.013 0.001 TRP B 338 HIS 0.001 0.000 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 3175) covalent geometry : angle 0.46780 / 0.24 ( 4324) hydrogen bonds : bond 0.04162 / 2.93 ( 257) hydrogen bonds : angle 4.52094 / 3.39 ( 771) *********************** 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 69 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.070 Fit side-chains REVERT: B 251 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: B 253 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7559 (mm-30) REVERT: B 331 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7770 (mtmm) outliers start: 15 outliers final: 7 residues processed: 61 average time/residue: 0.3551 time to fit residues: 22.4403 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 : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 136 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 1 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 30 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112002 restraints weight = 3669.234| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.79 r_work: 0.3290 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2039 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= 0.128 Angle : 0.464 4.983 4324 Z= 0.239 Chirality : 0.037 0.139 542 Planarity : 0.004 0.039 535 Dihedral : 3.193 16.461 440 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.26 % Allowed : 16.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.42), residues: 413 helix: 2.28 (0.28), residues: 335 sheet: -0.77 (1.16), residues: 20 loop : -0.64 (0.80), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.008 0.001 TYR B 334 PHE 0.010 0.001 PHE B 237 TRP 0.013 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 3175) covalent geometry : angle 0.46413 / 0.24 ( 4324) hydrogen bonds : bond 0.04075 / 2.86 ( 257) hydrogen bonds : angle 4.47059 / 3.35 ( 771) *********************** 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 61 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.119 Fit side-chains REVERT: B 251 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: B 331 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7722 (mtmm) outliers start: 14 outliers final: 7 residues processed: 54 average time/residue: 0.4538 time to fit residues: 25.3631 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 : 0.108 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111629 restraints weight = 3707.837| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.78 r_work: 0.3244 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2101 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= 0.131 Angle : 0.469 4.987 4324 Z= 0.240 Chirality : 0.038 0.139 542 Planarity : 0.004 0.039 535 Dihedral : 3.187 16.408 440 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.15 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.41), residues: 413 helix: 2.30 (0.28), residues: 339 sheet: -0.57 (1.16), residues: 21 loop : -0.30 (0.79), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.009 0.002 TYR B 334 PHE 0.010 0.001 PHE B 237 TRP 0.015 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 3175) covalent geometry : angle 0.46861 / 0.24 ( 4324) hydrogen bonds : bond 0.04073 / 2.86 ( 257) hydrogen bonds : angle 4.46760 / 3.34 ( 771) *********************** 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 60 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.129 Fit side-chains REVERT: B 251 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: B 331 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7744 (mtmm) REVERT: B 366 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7880 (mt-10) outliers start: 12 outliers final: 6 residues processed: 55 average time/residue: 0.4505 time to fit residues: 25.6472 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 : 0.141 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110031 restraints weight = 3777.940| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.80 r_work: 0.3216 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3175 Z= 0.154 Angle : 0.488 5.048 4324 Z= 0.250 Chirality : 0.039 0.142 542 Planarity : 0.004 0.038 535 Dihedral : 3.249 15.953 440 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.26 % Allowed : 16.11 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.41), residues: 413 helix: 2.28 (0.28), residues: 338 sheet: -0.62 (1.16), residues: 21 loop : -0.44 (0.77), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 98 TYR 0.011 0.002 TYR B 334 PHE 0.012 0.001 PHE B 237 TRP 0.016 0.002 TRP B 338 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 3175) covalent geometry : angle 0.48795 / 0.25 ( 4324) hydrogen bonds : bond 0.04280 / 3.00 ( 257) hydrogen bonds : angle 4.55546 / 3.40 ( 771) *********************** 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 61 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.121 Fit side-chains REVERT: B 251 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: B 366 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 475 ASP cc_start: 0.7570 (m-30) cc_final: 0.7317 (m-30) outliers start: 14 outliers final: 11 residues processed: 52 average time/residue: 0.4602 time to fit residues: 24.7403 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 : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 194 SER 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 13 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111477 restraints weight = 3792.511| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.82 r_work: 0.3248 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2161 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= 0.129 Angle : 0.466 4.938 4324 Z= 0.239 Chirality : 0.038 0.139 542 Planarity : 0.004 0.039 535 Dihedral : 3.202 16.050 440 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.04 % Allowed : 17.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.41), residues: 413 helix: 2.35 (0.28), residues: 338 sheet: -0.73 (1.15), residues: 21 loop : -0.49 (0.75), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 465 TYR 0.009 0.002 TYR B 334 PHE 0.010 0.001 PHE B 237 TRP 0.013 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 3175) covalent geometry : angle 0.46636 / 0.24 ( 4324) hydrogen bonds : bond 0.04044 / 2.84 ( 257) hydrogen bonds : angle 4.47539 / 3.35 ( 771) *********************** 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 58 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.072 Fit side-chains REVERT: B 251 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: B 475 ASP cc_start: 0.7462 (m-30) cc_final: 0.7181 (m-30) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.3959 time to fit residues: 21.2214 Evaluate side-chains 55 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.072 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 18 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.0270 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114102 restraints weight = 3730.992| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.81 r_work: 0.3282 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3175 Z= 0.108 Angle : 0.444 4.846 4324 Z= 0.227 Chirality : 0.037 0.133 542 Planarity : 0.004 0.038 535 Dihedral : 3.145 17.568 440 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.65 % Allowed : 17.33 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.41), residues: 413 helix: 2.52 (0.28), residues: 338 sheet: -0.67 (1.19), residues: 21 loop : -0.47 (0.75), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 465 TYR 0.008 0.001 TYR B 208 PHE 0.008 0.001 PHE B 237 TRP 0.012 0.001 TRP B 338 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 3175) covalent geometry : angle 0.44423 / 0.23 ( 4324) hydrogen bonds : bond 0.03707 / 2.61 ( 257) hydrogen bonds : angle 4.32986 / 3.24 ( 771) *********************** 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 62 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.074 Fit side-chains REVERT: B 251 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: B 475 ASP cc_start: 0.7399 (m-30) cc_final: 0.7108 (m-30) outliers start: 12 outliers final: 7 residues processed: 54 average time/residue: 0.3613 time to fit residues: 20.2282 Evaluate side-chains 55 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112097 restraints weight = 3667.821| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.81 r_work: 0.3254 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2301 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= 0.129 Angle : 0.466 4.926 4324 Z= 0.239 Chirality : 0.038 0.138 542 Planarity : 0.004 0.038 535 Dihedral : 3.143 16.163 440 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.74 % Allowed : 18.54 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.41), residues: 413 helix: 2.45 (0.28), residues: 338 sheet: -0.74 (1.20), residues: 21 loop : -0.45 (0.75), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 465 TYR 0.008 0.002 TYR B 334 PHE 0.011 0.001 PHE B 411 TRP 0.017 0.002 TRP B 338 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 3175) covalent geometry : angle 0.46578 / 0.24 ( 4324) hydrogen bonds : bond 0.03974 / 2.79 ( 257) hydrogen bonds : angle 4.40705 / 3.28 ( 771) ********************** 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 55 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.093 Fit side-chains REVERT: B 251 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: B 475 ASP cc_start: 0.7432 (m-30) cc_final: 0.7186 (m-30) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.3772 time to fit residues: 19.4236 Evaluate side-chains 51 residues out of total 329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 20 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.144647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110752 restraints weight = 3715.693| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.78 r_work: 0.3277 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2244 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= 0.146 Angle : 0.486 4.982 4324 Z= 0.250 Chirality : 0.038 0.144 542 Planarity : 0.004 0.038 535 Dihedral : 3.217 15.269 440 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.43 % Allowed : 18.54 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.41), residues: 413 helix: 2.35 (0.27), residues: 338 sheet: -0.75 (1.20), residues: 21 loop : -0.46 (0.75), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 189 TYR 0.010 0.002 TYR B 334 PHE 0.013 0.001 PHE B 411 TRP 0.018 0.002 TRP B 338 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 3175) covalent geometry : angle 0.48576 / 0.25 ( 4324) hydrogen bonds : bond 0.04174 / 2.93 ( 257) hydrogen bonds : angle 4.51047 / 3.36 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1176.52 seconds wall clock time: 20 minutes 55.38 seconds (1255.38 seconds total)