Starting phenix.real_space_refine on Fri May 9 14:38:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p7l_17536/05_2025/8p7l_17536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p7l_17536/05_2025/8p7l_17536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p7l_17536/05_2025/8p7l_17536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p7l_17536/05_2025/8p7l_17536.map" model { file = "/net/cci-nas-00/data/ceres_data/8p7l_17536/05_2025/8p7l_17536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p7l_17536/05_2025/8p7l_17536.cif" } resolution = 2.1 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1635 2.51 5 N 429 2.21 5 O 492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2568 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 194 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain breaks: 1 Chain: "J" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2300 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 270} Chain breaks: 2 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'WD9': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Time building chain proxies: 2.57, per 1000 atoms: 1.00 Number of scatterers: 2568 At special positions: 0 Unit cell: (59.85, 77.805, 68.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 492 8.00 N 429 7.00 C 1635 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: 0.70 Conformation dependent library (CDL) restraints added in 302.2 milliseconds 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 586 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 44.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 289 through 296 removed outlier: 3.808A pdb=" N CYS H 293 " --> pdb=" O SER H 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.915A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 removed outlier: 3.938A pdb=" N LEU J 222 " --> pdb=" O ASP J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 243 removed outlier: 3.592A pdb=" N LEU J 243 " --> pdb=" O MET J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.934A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 12 through 20 removed outlier: 6.612A pdb=" N LYS J 28 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N PHE J 17 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL J 26 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY J 19 " --> pdb=" O ALA J 24 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA J 24 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN J 36 " --> pdb=" O ASP J 31 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE J 87 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 99 hydrogen bonds defined for protein. 279 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: 0.61 Time building geometry restraints manager: 0.77 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: 808 1.34 - 1.46: 560 1.46 - 1.58: 1202 1.58 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 2589 Sorted by residual: bond pdb=" C9 WD9 J 401 " pdb=" N13 WD9 J 401 " ideal model delta sigma weight residual 1.326 1.463 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C7 WD9 J 401 " pdb=" O26 WD9 J 401 " ideal model delta sigma weight residual 1.322 1.407 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C5 WD9 J 401 " pdb=" N10 WD9 J 401 " ideal model delta sigma weight residual 1.379 1.298 0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" N10 WD9 J 401 " pdb=" N11 WD9 J 401 " ideal model delta sigma weight residual 1.342 1.410 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C27 WD9 J 401 " pdb=" C28 WD9 J 401 " ideal model delta sigma weight residual 1.535 1.487 0.048 2.00e-02 2.50e+03 5.79e+00 ... (remaining 2584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 3430 1.99 - 3.97: 69 3.97 - 5.96: 7 5.96 - 7.95: 2 7.95 - 9.93: 1 Bond angle restraints: 3509 Sorted by residual: angle pdb=" C27 WD9 J 401 " pdb=" O26 WD9 J 401 " pdb=" C7 WD9 J 401 " ideal model delta sigma weight residual 120.40 110.47 9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" N6 WD9 J 401 " pdb=" C7 WD9 J 401 " pdb=" N8 WD9 J 401 " ideal model delta sigma weight residual 127.26 119.88 7.38 3.00e+00 1.11e-01 6.06e+00 angle pdb=" C4 WD9 J 401 " pdb=" C12 WD9 J 401 " pdb=" N11 WD9 J 401 " ideal model delta sigma weight residual 114.13 107.60 6.53 3.00e+00 1.11e-01 4.74e+00 angle pdb=" CB GLU J 95 " pdb=" CG GLU J 95 " pdb=" CD GLU J 95 " ideal model delta sigma weight residual 112.60 115.94 -3.34 1.70e+00 3.46e-01 3.86e+00 angle pdb=" CA GLU J 62 " pdb=" CB GLU J 62 " pdb=" CG GLU J 62 " ideal model delta sigma weight residual 114.10 117.78 -3.68 2.00e+00 2.50e-01 3.39e+00 ... (remaining 3504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 1364 17.28 - 34.55: 145 34.55 - 51.83: 34 51.83 - 69.11: 4 69.11 - 86.38: 5 Dihedral angle restraints: 1552 sinusoidal: 645 harmonic: 907 Sorted by residual: dihedral pdb=" CB GLU J 126 " pdb=" CG GLU J 126 " pdb=" CD GLU J 126 " pdb=" OE1 GLU J 126 " ideal model delta sinusoidal sigma weight residual 0.00 86.38 -86.38 1 3.00e+01 1.11e-03 9.99e+00 dihedral pdb=" N VAL J 210 " pdb=" CA VAL J 210 " pdb=" CB VAL J 210 " pdb=" CG1 VAL J 210 " ideal model delta sinusoidal sigma weight residual 180.00 125.39 54.61 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" CG ARG J 309 " pdb=" CD ARG J 309 " pdb=" NE ARG J 309 " pdb=" CZ ARG J 309 " ideal model delta sinusoidal sigma weight residual 180.00 139.61 40.39 2 1.50e+01 4.44e-03 8.96e+00 ... (remaining 1549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 287 0.046 - 0.092: 79 0.092 - 0.138: 20 0.138 - 0.184: 0 0.184 - 0.230: 1 Chirality restraints: 387 Sorted by residual: chirality pdb=" C27 WD9 J 401 " pdb=" C28 WD9 J 401 " pdb=" C32 WD9 J 401 " pdb=" O26 WD9 J 401 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE J 255 " pdb=" N ILE J 255 " pdb=" C ILE J 255 " pdb=" CB ILE J 255 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE J 74 " pdb=" N ILE J 74 " pdb=" C ILE J 74 " pdb=" CB ILE J 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 384 not shown) Planarity restraints: 445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 279 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO H 280 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 280 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 280 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 210 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO J 211 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO J 211 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 211 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS J 71 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO J 72 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO J 72 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 72 " -0.016 5.00e-02 4.00e+02 ... (remaining 442 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 402 2.76 - 3.29: 2610 3.29 - 3.83: 4575 3.83 - 4.36: 5654 4.36 - 4.90: 9241 Nonbonded interactions: 22482 Sorted by model distance: nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR J 294 " pdb=" O HOH J 501 " model vdw 2.228 3.040 nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 402 " model vdw 2.260 3.040 nonbonded pdb=" O TRP J 177 " pdb=" O HOH J 502 " model vdw 2.266 3.040 nonbonded pdb=" O HOH J 514 " pdb=" O HOH J 533 " model vdw 2.269 3.040 ... (remaining 22477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.400 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 : 0.005 0.137 2589 Z= 0.261 Angle : 0.675 9.932 3509 Z= 0.325 Chirality : 0.045 0.230 387 Planarity : 0.005 0.040 445 Dihedral : 15.629 86.384 966 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.95 % Favored : 96.72 % Rotamer: Outliers : 1.11 % Allowed : 18.89 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.23 (0.47), residues: 305 helix: 0.13 (0.49), residues: 109 sheet: -0.93 (1.05), residues: 20 loop : -0.14 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.003 0.001 HIS J 259 PHE 0.015 0.002 PHE J 91 TYR 0.011 0.002 TYR J 127 ARG 0.008 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.10073 ( 99) hydrogen bonds : angle 7.07450 ( 279) covalent geometry : bond 0.00534 ( 2589) covalent geometry : angle 0.67525 ( 3509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.294 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 1.2392 time to fit residues: 64.8199 Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 242 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.184872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.165338 restraints weight = 2599.994| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.29 r_work: 0.3961 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2589 Z= 0.152 Angle : 0.574 4.666 3509 Z= 0.295 Chirality : 0.044 0.127 387 Planarity : 0.005 0.040 445 Dihedral : 6.665 57.387 361 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 3.33 % Allowed : 14.07 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.09 (0.47), residues: 305 helix: 0.55 (0.48), residues: 118 sheet: 0.02 (1.14), residues: 20 loop : -0.45 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.004 0.001 HIS J 259 PHE 0.020 0.002 PHE J 81 TYR 0.009 0.002 TYR H 248 ARG 0.006 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 99) hydrogen bonds : angle 5.37073 ( 279) covalent geometry : bond 0.00339 ( 2589) covalent geometry : angle 0.57413 ( 3509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.316 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 1.0546 time to fit residues: 54.2470 Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.185556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.165974 restraints weight = 2605.445| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.30 r_work: 0.3965 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2589 Z= 0.142 Angle : 0.557 4.438 3509 Z= 0.286 Chirality : 0.043 0.127 387 Planarity : 0.005 0.040 445 Dihedral : 6.124 59.012 360 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.95 % Favored : 96.72 % Rotamer: Outliers : 4.07 % Allowed : 13.33 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.10 (0.47), residues: 305 helix: 0.61 (0.47), residues: 118 sheet: -0.18 (1.12), residues: 21 loop : -0.49 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.003 0.001 HIS J 259 PHE 0.010 0.002 PHE J 91 TYR 0.008 0.001 TYR J 178 ARG 0.005 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 99) hydrogen bonds : angle 5.20563 ( 279) covalent geometry : bond 0.00316 ( 2589) covalent geometry : angle 0.55680 ( 3509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.319 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 52 average time/residue: 1.1747 time to fit residues: 62.6990 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.184675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.165182 restraints weight = 2627.999| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.28 r_work: 0.3959 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2589 Z= 0.164 Angle : 0.585 4.319 3509 Z= 0.302 Chirality : 0.044 0.128 387 Planarity : 0.005 0.040 445 Dihedral : 6.010 57.694 359 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 3.33 % Allowed : 13.33 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.13 (0.47), residues: 305 helix: 0.51 (0.47), residues: 118 sheet: -0.17 (1.13), residues: 21 loop : -0.45 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.013 0.002 PHE J 91 TYR 0.013 0.002 TYR J 27 ARG 0.006 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 99) hydrogen bonds : angle 5.23585 ( 279) covalent geometry : bond 0.00367 ( 2589) covalent geometry : angle 0.58452 ( 3509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.294 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 1.1553 time to fit residues: 58.1522 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.184429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.164853 restraints weight = 2636.258| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 1.28 r_work: 0.3954 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2589 Z= 0.172 Angle : 0.594 4.311 3509 Z= 0.307 Chirality : 0.045 0.129 387 Planarity : 0.005 0.041 445 Dihedral : 5.961 57.310 359 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 3.33 % Allowed : 14.07 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.20 (0.47), residues: 305 helix: 0.51 (0.47), residues: 118 sheet: -0.62 (1.09), residues: 20 loop : -0.47 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.004 0.001 HIS J 131 PHE 0.026 0.002 PHE J 81 TYR 0.011 0.002 TYR H 248 ARG 0.007 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 99) hydrogen bonds : angle 5.24655 ( 279) covalent geometry : bond 0.00386 ( 2589) covalent geometry : angle 0.59405 ( 3509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.296 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 1.2285 time to fit residues: 62.9720 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.185198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.165277 restraints weight = 2678.307| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.33 r_work: 0.3959 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3862 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2589 Z= 0.152 Angle : 0.580 4.272 3509 Z= 0.299 Chirality : 0.044 0.128 387 Planarity : 0.005 0.041 445 Dihedral : 5.781 56.157 359 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.93 % Favored : 95.74 % Rotamer: Outliers : 2.96 % Allowed : 14.81 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.06 (0.47), residues: 305 helix: 0.57 (0.47), residues: 118 sheet: -0.10 (1.14), residues: 21 loop : -0.41 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.003 0.001 HIS J 259 PHE 0.012 0.002 PHE J 91 TYR 0.009 0.002 TYR H 248 ARG 0.006 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 99) hydrogen bonds : angle 5.14910 ( 279) covalent geometry : bond 0.00342 ( 2589) covalent geometry : angle 0.57969 ( 3509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: J 309 ARG cc_start: 0.5807 (mpt180) cc_final: 0.5409 (mpt180) outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 1.4181 time to fit residues: 71.0784 Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.186505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.166486 restraints weight = 2721.399| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 1.34 r_work: 0.3971 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2589 Z= 0.131 Angle : 0.557 4.161 3509 Z= 0.286 Chirality : 0.043 0.127 387 Planarity : 0.005 0.041 445 Dihedral : 5.596 54.740 359 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.28 % Favored : 96.39 % Rotamer: Outliers : 3.33 % Allowed : 15.19 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.03 (0.47), residues: 305 helix: 0.67 (0.47), residues: 118 sheet: -0.11 (1.14), residues: 21 loop : -0.37 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.003 0.001 HIS J 259 PHE 0.011 0.002 PHE J 91 TYR 0.009 0.001 TYR J 178 ARG 0.007 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 99) hydrogen bonds : angle 5.03374 ( 279) covalent geometry : bond 0.00295 ( 2589) covalent geometry : angle 0.55741 ( 3509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.289 Fit side-chains REVERT: J 224 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6142 (mtt-85) REVERT: J 309 ARG cc_start: 0.5793 (mpt180) cc_final: 0.5579 (mpt180) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 1.2753 time to fit residues: 67.8419 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.186376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.166695 restraints weight = 2644.553| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.31 r_work: 0.3976 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2589 Z= 0.134 Angle : 0.570 4.160 3509 Z= 0.293 Chirality : 0.043 0.127 387 Planarity : 0.005 0.041 445 Dihedral : 5.554 55.042 359 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 2.59 % Allowed : 17.04 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.06 (0.47), residues: 305 helix: 0.70 (0.47), residues: 118 sheet: -0.16 (1.12), residues: 21 loop : -0.34 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.003 0.001 HIS J 259 PHE 0.018 0.002 PHE J 185 TYR 0.009 0.001 TYR H 248 ARG 0.007 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 99) hydrogen bonds : angle 5.01192 ( 279) covalent geometry : bond 0.00304 ( 2589) covalent geometry : angle 0.56975 ( 3509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: J 224 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6157 (mtt-85) REVERT: J 309 ARG cc_start: 0.5778 (mpt180) cc_final: 0.5563 (mpt180) outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 1.2315 time to fit residues: 59.2839 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.182933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.163637 restraints weight = 2611.880| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.26 r_work: 0.3943 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2589 Z= 0.218 Angle : 0.658 4.904 3509 Z= 0.343 Chirality : 0.046 0.134 387 Planarity : 0.006 0.040 445 Dihedral : 6.080 59.137 359 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.93 % Favored : 95.74 % Rotamer: Outliers : 2.59 % Allowed : 17.78 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.30 (0.47), residues: 305 helix: 0.44 (0.47), residues: 118 sheet: -0.79 (1.06), residues: 20 loop : -0.52 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.026 0.003 PHE J 81 TYR 0.014 0.002 TYR H 248 ARG 0.008 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 99) hydrogen bonds : angle 5.30303 ( 279) covalent geometry : bond 0.00494 ( 2589) covalent geometry : angle 0.65835 ( 3509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: J 224 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6084 (mtt-85) REVERT: J 309 ARG cc_start: 0.5831 (mpt180) cc_final: 0.5409 (mpt180) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 1.2806 time to fit residues: 60.3290 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.186194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.166468 restraints weight = 2650.676| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.32 r_work: 0.3972 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2589 Z= 0.135 Angle : 0.578 4.283 3509 Z= 0.298 Chirality : 0.043 0.126 387 Planarity : 0.005 0.040 445 Dihedral : 5.612 55.276 359 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 2.22 % Allowed : 18.15 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.04 (0.47), residues: 305 helix: 0.60 (0.47), residues: 118 sheet: -0.24 (1.12), residues: 21 loop : -0.38 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.004 0.001 HIS J 259 PHE 0.029 0.002 PHE J 81 TYR 0.013 0.002 TYR J 190 ARG 0.009 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 99) hydrogen bonds : angle 5.08309 ( 279) covalent geometry : bond 0.00306 ( 2589) covalent geometry : angle 0.57763 ( 3509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: J 224 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6133 (mtt-85) REVERT: J 309 ARG cc_start: 0.5760 (mpt180) cc_final: 0.5345 (mpt180) outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 1.2798 time to fit residues: 62.9447 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 224 ARG Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.187195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.167402 restraints weight = 2672.899| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 1.32 r_work: 0.3983 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2589 Z= 0.129 Angle : 0.575 5.020 3509 Z= 0.296 Chirality : 0.043 0.131 387 Planarity : 0.005 0.042 445 Dihedral : 5.441 53.785 359 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.93 % Favored : 95.74 % Rotamer: Outliers : 2.22 % Allowed : 18.15 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.09 (0.47), residues: 305 helix: 0.73 (0.47), residues: 118 sheet: -0.29 (1.13), residues: 21 loop : -0.31 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.004 0.001 HIS J 259 PHE 0.014 0.002 PHE J 185 TYR 0.017 0.002 TYR J 27 ARG 0.008 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 99) hydrogen bonds : angle 4.97152 ( 279) covalent geometry : bond 0.00292 ( 2589) covalent geometry : angle 0.57490 ( 3509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.37 seconds wall clock time: 50 minutes 35.93 seconds (3035.93 seconds total)