Starting phenix.real_space_refine on Wed Jun 3 11:05:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rws_54346/06_2026/9rws_54346.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rws_54346/06_2026/9rws_54346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rws_54346/06_2026/9rws_54346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rws_54346/06_2026/9rws_54346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rws_54346/06_2026/9rws_54346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rws_54346/06_2026/9rws_54346.map" } resolution = 3.28 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= 0.001 sd= 0.020 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 23 5.16 5 Na 1 4.78 5 C 2607 2.51 5 N 607 2.21 5 O 665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3903 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3894 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {' NA': 1, 'CHT': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 1.22, per 1000 atoms: 0.31 Number of scatterers: 3903 At special positions: 0 Unit cell: (70.4358, 62.6814, 82.7136, 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 23 16.00 Na 1 11.00 O 665 8.00 N 607 7.00 C 2607 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: 0.24 Conformation dependent library (CDL) restraints added in 185.8 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 79.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 22 through 43 removed outlier: 4.283A pdb=" N LEU A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 69 removed outlier: 3.723A pdb=" N THR A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.861A pdb=" N GLY A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.863A pdb=" N LYS A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 158 through 166 removed outlier: 3.712A pdb=" N GLY A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 193 Processing helix chain 'A' and resid 195 through 213 Processing helix chain 'A' and resid 220 through 246 removed outlier: 4.068A pdb=" N VAL A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.828A pdb=" N ASN A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 310 through 341 removed outlier: 4.162A pdb=" N VAL A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 368 through 402 removed outlier: 3.666A pdb=" N VAL A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 438 removed outlier: 3.701A pdb=" N ILE A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 466 removed outlier: 3.648A pdb=" N LEU A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 449 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.727A pdb=" N GLY A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 Processing sheet with id=AA1, first strand: chain 'A' and resid 504 through 505 289 hydrogen bonds defined for protein. 858 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: 0.65 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: 1153 1.34 - 1.46: 943 1.46 - 1.58: 1870 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 4008 Sorted by residual: bond pdb=" CG1 ILE A 227 " pdb=" CD1 ILE A 227 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.39e-01 bond pdb=" CG LEU A 190 " pdb=" CD2 LEU A 190 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.24e-01 bond pdb=" N LEU A 266 " pdb=" CA LEU A 266 " ideal model delta sigma weight residual 1.457 1.447 0.010 1.41e-02 5.03e+03 5.08e-01 bond pdb=" C ILE A 296 " pdb=" N PRO A 297 " ideal model delta sigma weight residual 1.334 1.350 -0.016 2.34e-02 1.83e+03 4.91e-01 bond pdb=" C SER A 115 " pdb=" N GLY A 116 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.74e-01 ... (remaining 4003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 5416 1.87 - 3.75: 47 3.75 - 5.62: 10 5.62 - 7.50: 1 7.50 - 9.37: 3 Bond angle restraints: 5477 Sorted by residual: angle pdb=" CA LEU A 531 " pdb=" CB LEU A 531 " pdb=" CG LEU A 531 " ideal model delta sigma weight residual 116.30 125.67 -9.37 3.50e+00 8.16e-02 7.17e+00 angle pdb=" CA LEU A 265 " pdb=" CB LEU A 265 " pdb=" CG LEU A 265 " ideal model delta sigma weight residual 116.30 125.46 -9.16 3.50e+00 8.16e-02 6.85e+00 angle pdb=" CA LEU A 495 " pdb=" CB LEU A 495 " pdb=" CG LEU A 495 " ideal model delta sigma weight residual 116.30 124.16 -7.86 3.50e+00 8.16e-02 5.05e+00 angle pdb=" CA TYR A 446 " pdb=" CB TYR A 446 " pdb=" CG TYR A 446 " ideal model delta sigma weight residual 113.90 117.84 -3.94 1.80e+00 3.09e-01 4.78e+00 angle pdb=" CA ILE A 402 " pdb=" C ILE A 402 " pdb=" N TYR A 403 " ideal model delta sigma weight residual 116.60 119.23 -2.63 1.45e+00 4.76e-01 3.28e+00 ... (remaining 5472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2006 17.67 - 35.35: 215 35.35 - 53.02: 48 53.02 - 70.70: 3 70.70 - 88.37: 2 Dihedral angle restraints: 2274 sinusoidal: 820 harmonic: 1454 Sorted by residual: dihedral pdb=" CA ASP A 343 " pdb=" CB ASP A 343 " pdb=" CG ASP A 343 " pdb=" OD1 ASP A 343 " ideal model delta sinusoidal sigma weight residual -30.00 -86.98 56.98 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CG ARG A 84 " pdb=" CD ARG A 84 " pdb=" NE ARG A 84 " pdb=" CZ ARG A 84 " ideal model delta sinusoidal sigma weight residual -90.00 -134.41 44.41 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CA ASP A 466 " pdb=" CB ASP A 466 " pdb=" CG ASP A 466 " pdb=" OD1 ASP A 466 " ideal model delta sinusoidal sigma weight residual -30.00 -85.34 55.34 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 2271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 367 0.024 - 0.049: 143 0.049 - 0.073: 91 0.073 - 0.098: 27 0.098 - 0.122: 10 Chirality restraints: 638 Sorted by residual: chirality pdb=" CB VAL A 37 " pdb=" CA VAL A 37 " pdb=" CG1 VAL A 37 " pdb=" CG2 VAL A 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA ILE A 504 " pdb=" N ILE A 504 " pdb=" C ILE A 504 " pdb=" CB ILE A 504 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA TYR A 446 " pdb=" N TYR A 446 " pdb=" C TYR A 446 " pdb=" CB TYR A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 635 not shown) Planarity restraints: 661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 511 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 512 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " -0.008 2.00e-02 2.50e+03 7.20e-03 1.04e+00 pdb=" CG TYR A 453 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 398 " -0.005 2.00e-02 2.50e+03 9.93e-03 9.85e-01 pdb=" C ALA A 398 " 0.017 2.00e-02 2.50e+03 pdb=" O ALA A 398 " -0.006 2.00e-02 2.50e+03 pdb=" N ALA A 399 " -0.006 2.00e-02 2.50e+03 ... (remaining 658 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 383 2.74 - 3.28: 3842 3.28 - 3.82: 7030 3.82 - 4.36: 7225 4.36 - 4.90: 13749 Nonbonded interactions: 32229 Sorted by model distance: nonbonded pdb=" OH TYR A 137 " pdb=" OG1 THR A 461 " model vdw 2.203 3.040 nonbonded pdb=" O THR A 112 " pdb=" OH TYR A 255 " model vdw 2.208 3.040 nonbonded pdb=" O VAL A 118 " pdb=" NE1 TRP A 284 " model vdw 2.275 3.120 nonbonded pdb=" OG SER A 177 " pdb=" OG SER A 390 " model vdw 2.297 3.040 nonbonded pdb=" O ILE A 525 " pdb=" OG SER A 529 " model vdw 2.310 3.040 ... (remaining 32224 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.110 Find NCS groups from input model: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 0.034 4008 Z= 0.106 Angle : 0.501 9.375 5477 Z= 0.235 Chirality : 0.037 0.122 638 Planarity : 0.003 0.030 661 Dihedral : 14.921 88.369 1354 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.25 % Allowed : 18.18 % Favored : 81.57 % 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: 2.46 (0.38), residues: 508 helix: 2.48 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.98 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.018 0.001 TYR A 453 PHE 0.015 0.001 PHE A 146 TRP 0.006 0.001 TRP A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 4008) covalent geometry : angle 0.50133 / 0.24 ( 5477) hydrogen bonds : bond 0.10178 / 6.23 ( 289) hydrogen bonds : angle 4.71183 / 3.42 ( 858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.090 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.0432 time to fit residues: 3.0915 Evaluate side-chains 50 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.0270 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.176988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143039 restraints weight = 4380.069| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.94 r_work: 0.3388 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4008 Z= 0.118 Angle : 0.490 7.484 5477 Z= 0.239 Chirality : 0.038 0.117 638 Planarity : 0.003 0.041 661 Dihedral : 4.154 54.996 552 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.53 % Allowed : 16.67 % Favored : 80.81 % 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: 2.62 (0.39), residues: 508 helix: 2.53 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.93 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.018 0.001 TYR A 446 PHE 0.009 0.001 PHE A 498 TRP 0.008 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 4008) covalent geometry : angle 0.48959 / 0.24 ( 5477) hydrogen bonds : bond 0.03604 / 2.35 ( 289) hydrogen bonds : angle 4.03129 / 2.89 ( 858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.083 Fit side-chains REVERT: A 236 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 259 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6261 (mtt) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.0590 time to fit residues: 4.8392 Evaluate side-chains 62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 0.0770 chunk 48 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.0170 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.178823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.144973 restraints weight = 4310.349| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.93 r_work: 0.3410 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4008 Z= 0.098 Angle : 0.477 7.586 5477 Z= 0.227 Chirality : 0.037 0.115 638 Planarity : 0.004 0.039 661 Dihedral : 4.175 57.729 552 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.02 % Allowed : 17.93 % Favored : 80.05 % 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: 2.79 (0.39), residues: 508 helix: 2.64 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.90 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 530 TYR 0.016 0.001 TYR A 446 PHE 0.010 0.001 PHE A 498 TRP 0.007 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 4008) covalent geometry : angle 0.47714 / 0.23 ( 5477) hydrogen bonds : bond 0.03256 / 2.10 ( 289) hydrogen bonds : angle 3.84647 / 2.79 ( 858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.105 Fit side-chains REVERT: A 236 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8051 (mp) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.0415 time to fit residues: 3.9620 Evaluate side-chains 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.171085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138899 restraints weight = 4170.036| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.79 r_work: 0.3397 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4008 Z= 0.130 Angle : 0.508 7.630 5477 Z= 0.241 Chirality : 0.038 0.123 638 Planarity : 0.003 0.040 661 Dihedral : 4.275 59.016 552 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.78 % Allowed : 18.18 % Favored : 79.04 % 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: 2.67 (0.39), residues: 508 helix: 2.57 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.96 (0.55), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 530 TYR 0.020 0.001 TYR A 446 PHE 0.010 0.001 PHE A 302 TRP 0.007 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 4008) covalent geometry : angle 0.50778 / 0.24 ( 5477) hydrogen bonds : bond 0.03438 / 2.23 ( 289) hydrogen bonds : angle 3.87550 / 2.82 ( 858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.130 Fit side-chains REVERT: A 210 TYR cc_start: 0.6986 (t80) cc_final: 0.6750 (t80) REVERT: A 259 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6273 (mtt) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.0480 time to fit residues: 4.3040 Evaluate side-chains 66 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 0.0010 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.178152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144017 restraints weight = 4366.469| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.94 r_work: 0.3383 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4008 Z= 0.116 Angle : 0.501 8.231 5477 Z= 0.237 Chirality : 0.038 0.122 638 Planarity : 0.003 0.041 661 Dihedral : 4.293 59.803 552 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.54 % Allowed : 17.93 % Favored : 78.54 % 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: 2.70 (0.39), residues: 508 helix: 2.60 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.98 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 530 TYR 0.018 0.001 TYR A 446 PHE 0.013 0.001 PHE A 146 TRP 0.007 0.001 TRP A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 4008) covalent geometry : angle 0.50089 / 0.24 ( 5477) hydrogen bonds : bond 0.03328 / 2.16 ( 289) hydrogen bonds : angle 3.83357 / 2.79 ( 858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.132 Fit side-chains REVERT: A 210 TYR cc_start: 0.7082 (t80) cc_final: 0.6848 (t80) REVERT: A 259 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6319 (mtt) outliers start: 14 outliers final: 11 residues processed: 70 average time/residue: 0.0544 time to fit residues: 5.0532 Evaluate side-chains 71 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.170049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137259 restraints weight = 4309.765| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.86 r_work: 0.3371 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4008 Z= 0.137 Angle : 0.522 8.363 5477 Z= 0.247 Chirality : 0.039 0.122 638 Planarity : 0.003 0.040 661 Dihedral : 4.321 59.672 552 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.54 % Allowed : 17.93 % Favored : 78.54 % 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: 2.63 (0.39), residues: 508 helix: 2.54 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -1.00 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 530 TYR 0.019 0.001 TYR A 446 PHE 0.011 0.001 PHE A 146 TRP 0.007 0.001 TRP A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 4008) covalent geometry : angle 0.52201 / 0.25 ( 5477) hydrogen bonds : bond 0.03483 / 2.25 ( 289) hydrogen bonds : angle 3.89249 / 2.84 ( 858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.142 Fit side-chains REVERT: A 210 TYR cc_start: 0.7058 (t80) cc_final: 0.6823 (t80) REVERT: A 259 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6355 (mtt) outliers start: 14 outliers final: 11 residues processed: 64 average time/residue: 0.0469 time to fit residues: 4.1572 Evaluate side-chains 66 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 462 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.180701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.147403 restraints weight = 4401.448| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.87 r_work: 0.3420 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4008 Z= 0.120 Angle : 0.514 9.087 5477 Z= 0.241 Chirality : 0.038 0.125 638 Planarity : 0.003 0.040 661 Dihedral : 4.304 59.299 552 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.79 % Allowed : 17.42 % Favored : 78.79 % 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: 2.66 (0.39), residues: 508 helix: 2.56 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -1.00 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 530 TYR 0.018 0.001 TYR A 446 PHE 0.012 0.001 PHE A 146 TRP 0.007 0.001 TRP A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 4008) covalent geometry : angle 0.51420 / 0.24 ( 5477) hydrogen bonds : bond 0.03353 / 2.17 ( 289) hydrogen bonds : angle 3.85176 / 2.81 ( 858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.132 Fit side-chains REVERT: A 210 TYR cc_start: 0.7044 (t80) cc_final: 0.6826 (t80) REVERT: A 259 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6307 (mtt) outliers start: 15 outliers final: 13 residues processed: 66 average time/residue: 0.0451 time to fit residues: 4.1029 Evaluate side-chains 68 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.0060 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.174644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.141691 restraints weight = 4352.878| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.85 r_work: 0.3375 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4008 Z= 0.115 Angle : 0.516 9.710 5477 Z= 0.240 Chirality : 0.038 0.122 638 Planarity : 0.003 0.040 661 Dihedral : 4.283 58.871 552 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.03 % Allowed : 18.18 % Favored : 78.79 % 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: 2.69 (0.39), residues: 508 helix: 2.59 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.99 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 530 TYR 0.018 0.001 TYR A 446 PHE 0.013 0.001 PHE A 146 TRP 0.007 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 4008) covalent geometry : angle 0.51624 / 0.24 ( 5477) hydrogen bonds : bond 0.03301 / 2.13 ( 289) hydrogen bonds : angle 3.81468 / 2.79 ( 858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.090 Fit side-chains REVERT: A 210 TYR cc_start: 0.7053 (t80) cc_final: 0.6849 (t80) REVERT: A 259 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6299 (mtt) outliers start: 12 outliers final: 11 residues processed: 62 average time/residue: 0.0415 time to fit residues: 3.5312 Evaluate side-chains 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 7 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 6 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.175137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142112 restraints weight = 4350.895| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.85 r_work: 0.3386 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4008 Z= 0.112 Angle : 0.519 9.996 5477 Z= 0.240 Chirality : 0.038 0.129 638 Planarity : 0.003 0.040 661 Dihedral : 4.262 58.497 552 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.03 % Allowed : 18.69 % Favored : 78.28 % 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: 2.72 (0.39), residues: 508 helix: 2.61 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.96 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 530 TYR 0.017 0.001 TYR A 446 PHE 0.010 0.001 PHE A 498 TRP 0.007 0.001 TRP A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 4008) covalent geometry : angle 0.51862 / 0.24 ( 5477) hydrogen bonds : bond 0.03245 / 2.10 ( 289) hydrogen bonds : angle 3.78661 / 2.76 ( 858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.138 Fit side-chains REVERT: A 259 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6276 (mtt) outliers start: 12 outliers final: 11 residues processed: 62 average time/residue: 0.0487 time to fit residues: 4.1706 Evaluate side-chains 65 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 7 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.0470 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.174056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141082 restraints weight = 4379.556| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.84 r_work: 0.3380 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4008 Z= 0.119 Angle : 0.528 10.415 5477 Z= 0.244 Chirality : 0.038 0.131 638 Planarity : 0.003 0.041 661 Dihedral : 4.255 58.290 552 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.03 % Allowed : 18.69 % Favored : 78.28 % 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: 2.72 (0.39), residues: 508 helix: 2.60 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.96 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 530 TYR 0.018 0.001 TYR A 446 PHE 0.010 0.001 PHE A 513 TRP 0.007 0.001 TRP A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 4008) covalent geometry : angle 0.52771 / 0.24 ( 5477) hydrogen bonds : bond 0.03304 / 2.14 ( 289) hydrogen bonds : angle 3.80258 / 2.78 ( 858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.133 Fit side-chains REVERT: A 259 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6307 (mtt) REVERT: A 387 MET cc_start: 0.7309 (tpt) cc_final: 0.6909 (tpt) outliers start: 12 outliers final: 11 residues processed: 62 average time/residue: 0.0482 time to fit residues: 4.1710 Evaluate side-chains 65 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 7 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.0060 chunk 37 optimal weight: 7.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.173391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.140455 restraints weight = 4355.552| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.83 r_work: 0.3370 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4008 Z= 0.125 Angle : 0.533 10.818 5477 Z= 0.246 Chirality : 0.038 0.129 638 Planarity : 0.003 0.041 661 Dihedral : 4.269 58.205 552 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.54 % Allowed : 18.18 % Favored : 78.28 % 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: 2.69 (0.39), residues: 508 helix: 2.58 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.97 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 530 TYR 0.018 0.001 TYR A 446 PHE 0.010 0.001 PHE A 513 TRP 0.008 0.001 TRP A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4008) covalent geometry : angle 0.53319 / 0.25 ( 5477) hydrogen bonds : bond 0.03370 / 2.18 ( 289) hydrogen bonds : angle 3.82379 / 2.79 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1075.97 seconds wall clock time: 19 minutes 16.95 seconds (1156.95 seconds total)