Starting phenix.real_space_refine on Sun Apr 27 00:16:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tej_41188/04_2025/8tej_41188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tej_41188/04_2025/8tej_41188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tej_41188/04_2025/8tej_41188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tej_41188/04_2025/8tej_41188.map" model { file = "/net/cci-nas-00/data/ceres_data/8tej_41188/04_2025/8tej_41188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tej_41188/04_2025/8tej_41188.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 26 5.16 5 C 2555 2.51 5 N 645 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3925 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3903 Classifications: {'peptide': 494} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 467} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Time building chain proxies: 3.59, per 1000 atoms: 0.91 Number of scatterers: 3925 At special positions: 0 Unit cell: (64.74, 78.02, 93.79, 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 26 16.00 P 1 15.00 O 698 8.00 N 645 7.00 C 2555 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: 1.04 Conformation dependent library (CDL) restraints added in 473.5 milliseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 912 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 77.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.671A pdb=" N ALA A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 36 through 62 Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.633A pdb=" N ALA A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 145 through 151 removed outlier: 4.172A pdb=" N ASN A 149 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 151' Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.681A pdb=" N GLY A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 219 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 228 through 251 removed outlier: 6.277A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.447A pdb=" N GLY A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.730A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 297 through 319 removed outlier: 3.540A pdb=" N SER A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 359 through 391 removed outlier: 3.706A pdb=" N LYS A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 424 through 431 removed outlier: 3.524A pdb=" N THR A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 4.379A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 464 through 477 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.721A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 259 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1209 1.34 - 1.46: 574 1.46 - 1.57: 2168 1.57 - 1.69: 3 1.69 - 1.81: 45 Bond restraints: 3999 Sorted by residual: bond pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O3P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" O2P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.528 1.607 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" O1P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.525 1.479 0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" N TPO A 410 " pdb=" CA TPO A 410 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 ... (remaining 3994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 5374 2.30 - 4.60: 47 4.60 - 6.90: 3 6.90 - 9.20: 0 9.20 - 11.50: 2 Bond angle restraints: 5426 Sorted by residual: angle pdb=" CB TPO A 410 " pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 119.31 107.81 11.50 3.00e+00 1.11e-01 1.47e+01 angle pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " pdb=" O1P TPO A 410 " ideal model delta sigma weight residual 100.43 110.03 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C PRO A 7 " pdb=" N PHE A 8 " pdb=" CA PHE A 8 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.21e+00 angle pdb=" N GLY A 395 " pdb=" CA GLY A 395 " pdb=" C GLY A 395 " ideal model delta sigma weight residual 113.18 108.47 4.71 2.37e+00 1.78e-01 3.95e+00 angle pdb=" O1P TPO A 410 " pdb=" P TPO A 410 " pdb=" O3P TPO A 410 " ideal model delta sigma weight residual 115.11 109.22 5.89 3.00e+00 1.11e-01 3.85e+00 ... (remaining 5421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 1995 16.02 - 32.04: 245 32.04 - 48.06: 82 48.06 - 64.08: 36 64.08 - 80.10: 7 Dihedral angle restraints: 2365 sinusoidal: 946 harmonic: 1419 Sorted by residual: dihedral pdb=" CA ILE A 291 " pdb=" C ILE A 291 " pdb=" N VAL A 292 " pdb=" CA VAL A 292 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLY A 395 " pdb=" C GLY A 395 " pdb=" N GLN A 396 " pdb=" CA GLN A 396 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ILE A 295 " pdb=" CB ILE A 295 " pdb=" CG1 ILE A 295 " pdb=" CD1 ILE A 295 " ideal model delta sinusoidal sigma weight residual 60.00 119.76 -59.76 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 396 0.026 - 0.052: 128 0.052 - 0.079: 62 0.079 - 0.105: 19 0.105 - 0.131: 11 Chirality restraints: 616 Sorted by residual: chirality pdb=" CA ILE A 181 " pdb=" N ILE A 181 " pdb=" C ILE A 181 " pdb=" CB ILE A 181 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA VAL A 289 " pdb=" N VAL A 289 " pdb=" C VAL A 289 " pdb=" CB VAL A 289 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE A 92 " pdb=" N ILE A 92 " pdb=" C ILE A 92 " pdb=" CB ILE A 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 613 not shown) Planarity restraints: 674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 247 " 0.005 2.00e-02 2.50e+03 9.47e-03 8.96e-01 pdb=" C TRP A 247 " -0.016 2.00e-02 2.50e+03 pdb=" O TRP A 247 " 0.006 2.00e-02 2.50e+03 pdb=" N THR A 248 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 258 " -0.015 5.00e-02 4.00e+02 2.22e-02 7.86e-01 pdb=" N PRO A 259 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 361 " -0.014 5.00e-02 4.00e+02 2.14e-02 7.30e-01 pdb=" N PRO A 362 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " -0.012 5.00e-02 4.00e+02 ... (remaining 671 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 25 2.57 - 3.15: 3166 3.15 - 3.73: 6231 3.73 - 4.32: 8524 4.32 - 4.90: 14206 Nonbonded interactions: 32152 Sorted by model distance: nonbonded pdb=" OH TYR A 405 " pdb=" OE2 GLU A 459 " model vdw 1.984 3.040 nonbonded pdb=" OD2 ASP A 335 " pdb=" O HOH A 801 " model vdw 2.033 3.040 nonbonded pdb=" OH TYR A 22 " pdb=" O ILE A 84 " model vdw 2.042 3.040 nonbonded pdb=" O GLY A 261 " pdb=" O HOH A 802 " model vdw 2.085 3.040 nonbonded pdb=" O LYS A 424 " pdb=" OG1 THR A 427 " model vdw 2.171 3.040 ... (remaining 32147 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: 2.730 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.300 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.004 0.108 3999 Z= 0.188 Angle : 0.572 11.496 5426 Z= 0.276 Chirality : 0.036 0.131 616 Planarity : 0.003 0.027 674 Dihedral : 17.726 80.101 1453 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.87 % Allowed : 20.57 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.14 (0.38), residues: 485 helix: 2.11 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -0.15 (0.51), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.006 0.001 PHE A 107 TYR 0.011 0.001 TYR A 495 ARG 0.005 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.11922 ( 259) hydrogen bonds : angle 5.03880 ( 753) covalent geometry : bond 0.00394 ( 3999) covalent geometry : angle 0.57239 ( 5426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.398 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 1.2287 time to fit residues: 69.9283 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116887 restraints weight = 4283.560| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.53 r_work: 0.3142 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3999 Z= 0.134 Angle : 0.511 5.633 5426 Z= 0.260 Chirality : 0.039 0.168 616 Planarity : 0.004 0.032 674 Dihedral : 6.187 43.321 547 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.87 % Allowed : 17.94 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.15 (0.37), residues: 485 helix: 2.09 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -0.14 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 131 HIS 0.003 0.001 HIS A 312 PHE 0.009 0.001 PHE A 509 TYR 0.012 0.001 TYR A 495 ARG 0.003 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 259) hydrogen bonds : angle 4.46579 ( 753) covalent geometry : bond 0.00293 ( 3999) covalent geometry : angle 0.51099 ( 5426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.461 Fit side-chains REVERT: A 385 ARG cc_start: 0.6882 (mtt90) cc_final: 0.6674 (mmt90) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 1.3173 time to fit residues: 77.6491 Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.119624 restraints weight = 4275.168| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.52 r_work: 0.3203 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3999 Z= 0.117 Angle : 0.479 5.547 5426 Z= 0.243 Chirality : 0.038 0.158 616 Planarity : 0.004 0.033 674 Dihedral : 5.194 36.142 538 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.83 % Allowed : 18.66 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 (0.37), residues: 485 helix: 2.21 (0.27), residues: 338 sheet: None (None), residues: 0 loop : -0.06 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 131 HIS 0.003 0.001 HIS A 312 PHE 0.007 0.001 PHE A 509 TYR 0.011 0.001 TYR A 495 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 259) hydrogen bonds : angle 4.29098 ( 753) covalent geometry : bond 0.00246 ( 3999) covalent geometry : angle 0.47862 ( 5426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.445 Fit side-chains REVERT: A 35 ARG cc_start: 0.7409 (mtt180) cc_final: 0.6668 (mpp-170) REVERT: A 219 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8439 (mmm160) REVERT: A 295 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8088 (mp) outliers start: 16 outliers final: 7 residues processed: 62 average time/residue: 1.3162 time to fit residues: 84.3738 Evaluate side-chains 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116336 restraints weight = 4266.382| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.52 r_work: 0.3193 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3999 Z= 0.147 Angle : 0.527 5.853 5426 Z= 0.267 Chirality : 0.040 0.170 616 Planarity : 0.004 0.033 674 Dihedral : 5.338 38.194 538 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.11 % Allowed : 20.57 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.37), residues: 485 helix: 2.01 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -0.15 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 26 HIS 0.004 0.001 HIS A 312 PHE 0.010 0.001 PHE A 509 TYR 0.014 0.002 TYR A 495 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.05133 ( 259) hydrogen bonds : angle 4.39617 ( 753) covalent geometry : bond 0.00331 ( 3999) covalent geometry : angle 0.52673 ( 5426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.476 Fit side-chains REVERT: A 295 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8110 (mp) REVERT: A 463 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.7447 (pp30) outliers start: 13 outliers final: 7 residues processed: 57 average time/residue: 1.6485 time to fit residues: 97.0524 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.118623 restraints weight = 4406.598| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.55 r_work: 0.3196 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3999 Z= 0.120 Angle : 0.491 6.841 5426 Z= 0.247 Chirality : 0.038 0.157 616 Planarity : 0.004 0.032 674 Dihedral : 4.795 35.490 536 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.63 % Allowed : 20.81 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.18 (0.37), residues: 485 helix: 2.11 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -0.09 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 131 HIS 0.003 0.001 HIS A 312 PHE 0.007 0.001 PHE A 509 TYR 0.012 0.001 TYR A 495 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 259) hydrogen bonds : angle 4.27207 ( 753) covalent geometry : bond 0.00256 ( 3999) covalent geometry : angle 0.49051 ( 5426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.554 Fit side-chains REVERT: A 35 ARG cc_start: 0.7539 (mtt180) cc_final: 0.6768 (mpp-170) REVERT: A 295 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8093 (mp) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 1.9827 time to fit residues: 115.7822 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117653 restraints weight = 4325.857| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.54 r_work: 0.3186 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3999 Z= 0.130 Angle : 0.506 6.497 5426 Z= 0.255 Chirality : 0.039 0.162 616 Planarity : 0.004 0.032 674 Dihedral : 4.825 35.864 536 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.11 % Allowed : 20.10 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.17 (0.37), residues: 485 helix: 2.13 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -0.07 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.007 0.001 PHE A 509 TYR 0.013 0.001 TYR A 495 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 259) hydrogen bonds : angle 4.30006 ( 753) covalent geometry : bond 0.00284 ( 3999) covalent geometry : angle 0.50580 ( 5426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.787 Fit side-chains REVERT: A 16 LYS cc_start: 0.7355 (mtpp) cc_final: 0.6899 (pttp) REVERT: A 115 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5724 (mp0) REVERT: A 295 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 463 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7549 (pp30) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 1.4704 time to fit residues: 83.9067 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119876 restraints weight = 4303.312| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.53 r_work: 0.3206 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3999 Z= 0.115 Angle : 0.478 6.254 5426 Z= 0.241 Chirality : 0.038 0.157 616 Planarity : 0.004 0.032 674 Dihedral : 4.593 33.726 535 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.39 % Allowed : 21.53 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.31 (0.38), residues: 485 helix: 2.21 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.03 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.007 0.001 PHE A 192 TYR 0.012 0.001 TYR A 495 ARG 0.005 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 259) hydrogen bonds : angle 4.21787 ( 753) covalent geometry : bond 0.00241 ( 3999) covalent geometry : angle 0.47828 ( 5426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.397 Fit side-chains REVERT: A 16 LYS cc_start: 0.7356 (mtpp) cc_final: 0.6963 (pttp) REVERT: A 35 ARG cc_start: 0.7527 (mtt180) cc_final: 0.6755 (mpp-170) REVERT: A 115 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5678 (mp0) REVERT: A 295 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8067 (mp) REVERT: A 463 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7521 (pp30) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 1.3203 time to fit residues: 75.3240 Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 0.0670 chunk 27 optimal weight: 0.0000 chunk 33 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 0.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.152091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122186 restraints weight = 4322.695| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.54 r_work: 0.3253 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3999 Z= 0.097 Angle : 0.441 5.568 5426 Z= 0.222 Chirality : 0.037 0.152 616 Planarity : 0.004 0.032 674 Dihedral : 4.333 29.405 535 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.44 % Allowed : 22.73 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.67 (0.38), residues: 485 helix: 2.49 (0.28), residues: 332 sheet: None (None), residues: 0 loop : 0.17 (0.50), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 131 HIS 0.002 0.001 HIS A 407 PHE 0.005 0.001 PHE A 498 TYR 0.009 0.001 TYR A 495 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 259) hydrogen bonds : angle 4.07874 ( 753) covalent geometry : bond 0.00190 ( 3999) covalent geometry : angle 0.44142 ( 5426) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 1.069 Fit side-chains REVERT: A 16 LYS cc_start: 0.7303 (mtpp) cc_final: 0.6950 (pttp) REVERT: A 35 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6524 (mpp-170) REVERT: A 113 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7618 (mmt90) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 1.9737 time to fit residues: 110.2187 Evaluate side-chains 50 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 0.0000 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116833 restraints weight = 4280.919| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.53 r_work: 0.3147 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3999 Z= 0.144 Angle : 0.531 6.787 5426 Z= 0.266 Chirality : 0.040 0.162 616 Planarity : 0.004 0.031 674 Dihedral : 4.356 32.248 533 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.67 % Allowed : 22.49 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.22 (0.38), residues: 485 helix: 2.14 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.02 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 26 HIS 0.004 0.001 HIS A 312 PHE 0.009 0.001 PHE A 509 TYR 0.013 0.002 TYR A 495 ARG 0.007 0.001 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 259) hydrogen bonds : angle 4.30560 ( 753) covalent geometry : bond 0.00322 ( 3999) covalent geometry : angle 0.53070 ( 5426) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.394 Fit side-chains REVERT: A 16 LYS cc_start: 0.7376 (mtpp) cc_final: 0.6994 (pttp) REVERT: A 463 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.7551 (pp30) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 1.2884 time to fit residues: 63.9396 Evaluate side-chains 47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.149069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118752 restraints weight = 4350.570| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.54 r_work: 0.3215 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3999 Z= 0.124 Angle : 0.501 6.448 5426 Z= 0.251 Chirality : 0.038 0.158 616 Planarity : 0.004 0.032 674 Dihedral : 4.241 28.879 533 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.44 % Allowed : 22.73 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.24 (0.37), residues: 485 helix: 2.16 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.00 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.007 0.001 PHE A 159 TYR 0.012 0.001 TYR A 495 ARG 0.007 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 259) hydrogen bonds : angle 4.26305 ( 753) covalent geometry : bond 0.00268 ( 3999) covalent geometry : angle 0.50143 ( 5426) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.449 Fit side-chains REVERT: A 16 LYS cc_start: 0.7380 (mtpp) cc_final: 0.6991 (pttp) REVERT: A 295 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8001 (mp) REVERT: A 396 GLN cc_start: 0.6899 (tt0) cc_final: 0.6640 (tt0) REVERT: A 463 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.7519 (pp30) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 1.3186 time to fit residues: 68.2360 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.117256 restraints weight = 4276.498| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.53 r_work: 0.3197 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3999 Z= 0.125 Angle : 0.503 6.450 5426 Z= 0.252 Chirality : 0.039 0.158 616 Planarity : 0.004 0.032 674 Dihedral : 4.282 30.744 533 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.44 % Allowed : 22.73 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.24 (0.38), residues: 485 helix: 2.16 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -0.00 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.007 0.001 PHE A 509 TYR 0.012 0.001 TYR A 495 ARG 0.007 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 259) hydrogen bonds : angle 4.26909 ( 753) covalent geometry : bond 0.00271 ( 3999) covalent geometry : angle 0.50300 ( 5426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3754.78 seconds wall clock time: 67 minutes 19.45 seconds (4039.45 seconds total)