Starting phenix.real_space_refine on Fri Oct 10 11:07:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qta_18647/10_2025/8qta_18647.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qta_18647/10_2025/8qta_18647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qta_18647/10_2025/8qta_18647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qta_18647/10_2025/8qta_18647.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qta_18647/10_2025/8qta_18647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qta_18647/10_2025/8qta_18647.map" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.099 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 5 5.49 5 S 11 5.16 5 C 2276 2.51 5 N 555 2.21 5 O 623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3472 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3258 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 214 Unusual residues: {'FAD': 1, 'HEM': 2, 'NDP': 1} Classifications: {'undetermined': 4, 'water': 27} Link IDs: {None: 30} Time building chain proxies: 0.97, per 1000 atoms: 0.28 Number of scatterers: 3472 At special positions: 0 Unit cell: (57.9384, 65.7378, 94.707, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 11 16.00 P 5 15.00 O 623 8.00 N 555 7.00 C 2276 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 98.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 53.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 7 through 29 Processing helix chain 'A' and resid 32 through 48 Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.587A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 88 Processing helix chain 'A' and resid 94 through 116 removed outlier: 3.690A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 147 Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.611A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.780A pdb=" N TYR A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.728A pdb=" N ALA A 325 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 372 through 387 removed outlier: 3.673A pdb=" N GLN A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 236 removed outlier: 3.792A pdb=" N LYS A 268 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR A 186 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLY A 188 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER A 208 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 190 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS A 206 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A 192 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLN A 243 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 347 removed outlier: 6.879A pdb=" N ASN A 286 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR A 368 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 288 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N CYS A 370 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 290 " --> pdb=" O CYS A 370 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 549 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: 0.46 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 1304 1.38 - 1.56: 2222 1.56 - 1.74: 8 1.74 - 1.93: 22 1.93 - 2.11: 7 Bond restraints: 3563 Sorted by residual: bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.624 0.209 3.80e-02 6.93e+02 3.02e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.600 0.157 3.50e-02 8.16e+02 2.02e+01 bond pdb=" C3C HEM A 503 " pdb=" CAC HEM A 503 " ideal model delta sigma weight residual 1.544 1.467 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C3B HEM A 503 " pdb=" CAB HEM A 503 " ideal model delta sigma weight residual 1.544 1.467 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O5B FAD A 502 " pdb=" PA FAD A 502 " ideal model delta sigma weight residual 1.634 1.560 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 3558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 4831 4.67 - 9.33: 37 9.33 - 14.00: 1 14.00 - 18.67: 2 18.67 - 23.34: 1 Bond angle restraints: 4872 Sorted by residual: angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 131.08 -23.34 1.95e+00 2.62e-01 1.43e+02 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 118.26 -14.42 1.91e+00 2.73e-01 5.67e+01 angle pdb=" C5D NDP A 501 " pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 104.93 121.79 -16.86 2.66e+00 1.41e-01 4.02e+01 angle pdb=" N ASP A 254 " pdb=" CA ASP A 254 " pdb=" CB ASP A 254 " ideal model delta sigma weight residual 110.33 102.70 7.63 1.50e+00 4.44e-01 2.59e+01 angle pdb=" O2N NDP A 501 " pdb=" PN NDP A 501 " pdb=" O5D NDP A 501 " ideal model delta sigma weight residual 100.52 109.84 -9.32 1.91e+00 2.74e-01 2.38e+01 ... (remaining 4867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.91: 1709 19.91 - 39.83: 211 39.83 - 59.74: 69 59.74 - 79.65: 14 79.65 - 99.56: 7 Dihedral angle restraints: 2010 sinusoidal: 848 harmonic: 1162 Sorted by residual: dihedral pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " ideal model delta sinusoidal sigma weight residual 175.04 75.48 99.56 1 3.00e+01 1.11e-03 1.24e+01 dihedral pdb=" C2D HEM A 503 " pdb=" C3D HEM A 503 " pdb=" CAD HEM A 503 " pdb=" CBD HEM A 503 " ideal model delta sinusoidal sigma weight residual -180.00 -99.38 -80.62 2 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" C1A HEM A 504 " pdb=" C2A HEM A 504 " pdb=" CAA HEM A 504 " pdb=" CBA HEM A 504 " ideal model delta sinusoidal sigma weight residual 180.00 101.87 78.13 2 2.00e+01 2.50e-03 1.15e+01 ... (remaining 2007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 390 0.045 - 0.090: 83 0.090 - 0.134: 29 0.134 - 0.179: 4 0.179 - 0.224: 3 Chirality restraints: 509 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C3B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" C4B NDP A 501 " pdb=" O3B NDP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2D NDP A 501 " pdb=" C1D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" O2D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 506 not shown) Planarity restraints: 580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 501 " -0.106 2.00e-02 2.50e+03 6.76e-02 5.71e+01 pdb=" C3N NDP A 501 " -0.025 2.00e-02 2.50e+03 pdb=" C4N NDP A 501 " -0.013 2.00e-02 2.50e+03 pdb=" C7N NDP A 501 " 0.061 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM A 503 " 0.003 2.00e-02 2.50e+03 1.58e-02 5.61e+00 pdb=" C2C HEM A 503 " -0.005 2.00e-02 2.50e+03 pdb=" C3C HEM A 503 " -0.002 2.00e-02 2.50e+03 pdb=" C4C HEM A 503 " -0.010 2.00e-02 2.50e+03 pdb=" CAC HEM A 503 " -0.002 2.00e-02 2.50e+03 pdb=" CHC HEM A 503 " 0.019 2.00e-02 2.50e+03 pdb=" CHD HEM A 503 " 0.027 2.00e-02 2.50e+03 pdb=" CMC HEM A 503 " 0.003 2.00e-02 2.50e+03 pdb=" NC HEM A 503 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM A 503 " 0.006 2.00e-02 2.50e+03 1.44e-02 4.64e+00 pdb=" C2A HEM A 503 " 0.004 2.00e-02 2.50e+03 pdb=" C3A HEM A 503 " 0.001 2.00e-02 2.50e+03 pdb=" C4A HEM A 503 " 0.001 2.00e-02 2.50e+03 pdb=" CAA HEM A 503 " 0.000 2.00e-02 2.50e+03 pdb=" CHA HEM A 503 " -0.023 2.00e-02 2.50e+03 pdb=" CHB HEM A 503 " -0.019 2.00e-02 2.50e+03 pdb=" CMA HEM A 503 " -0.000 2.00e-02 2.50e+03 pdb=" NA HEM A 503 " 0.030 2.00e-02 2.50e+03 ... (remaining 577 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 110 2.70 - 3.25: 3175 3.25 - 3.80: 5818 3.80 - 4.35: 8071 4.35 - 4.90: 12933 Nonbonded interactions: 30107 Sorted by model distance: nonbonded pdb=" NE2 HIS A 142 " pdb="FE HEM A 503 " model vdw 2.155 3.080 nonbonded pdb=" NE2 HIS A 129 " pdb="FE HEM A 504 " model vdw 2.212 3.080 nonbonded pdb=" O SER A 238 " pdb=" OG SER A 238 " model vdw 2.220 3.040 nonbonded pdb=" O HOH A 613 " pdb=" O HOH A 617 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP A 254 " pdb=" O HOH A 601 " model vdw 2.242 3.040 ... (remaining 30102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.590 Find NCS groups from input model: 0.010 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:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.009 0.209 3565 Z= 0.365 Angle : 0.967 23.336 4872 Z= 0.430 Chirality : 0.045 0.224 509 Planarity : 0.004 0.068 580 Dihedral : 20.123 99.565 1270 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.16 % Allowed : 26.88 % Favored : 71.97 % 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 aren not related in a simple way. whole: -0.55 (0.39), residues: 397 helix: -0.29 (0.34), residues: 200 sheet: 0.66 (0.54), residues: 87 loop : -1.06 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.013 0.001 TYR A 275 PHE 0.009 0.001 PHE A 218 TRP 0.007 0.001 TRP A 125 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00940 ( 3563) covalent geometry : angle 0.96657 ( 4872) hydrogen bonds : bond 0.22562 ( 187) hydrogen bonds : angle 7.63902 ( 549) Misc. bond : bond 0.02040 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 394 TYR cc_start: 0.6008 (p90) cc_final: 0.5495 (p90) outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 0.5937 time to fit residues: 32.3899 Evaluate side-chains 52 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 370 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.0040 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.148481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118935 restraints weight = 3452.387| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.61 r_work: 0.3233 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.191 3565 Z= 0.139 Angle : 0.640 13.931 4872 Z= 0.281 Chirality : 0.041 0.155 509 Planarity : 0.003 0.030 580 Dihedral : 11.652 85.486 516 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.02 % Allowed : 27.17 % Favored : 70.81 % 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 aren not related in a simple way. whole: 0.63 (0.41), residues: 397 helix: 1.24 (0.35), residues: 201 sheet: 0.20 (0.54), residues: 93 loop : -0.85 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.013 0.001 TYR A 275 PHE 0.009 0.001 PHE A 218 TRP 0.006 0.001 TRP A 25 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3563) covalent geometry : angle 0.64023 ( 4872) hydrogen bonds : bond 0.04519 ( 187) hydrogen bonds : angle 4.76793 ( 549) Misc. bond : bond 0.16141 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7563 (p0) REVERT: A 320 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6614 (mpt-90) outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 0.6299 time to fit residues: 34.3141 Evaluate side-chains 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.0570 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120746 restraints weight = 3451.859| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.61 r_work: 0.3266 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 3565 Z= 0.117 Angle : 0.602 12.882 4872 Z= 0.261 Chirality : 0.040 0.147 509 Planarity : 0.003 0.027 580 Dihedral : 10.767 77.258 515 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.31 % Allowed : 26.59 % Favored : 71.10 % 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 aren not related in a simple way. whole: 1.01 (0.42), residues: 397 helix: 1.73 (0.36), residues: 201 sheet: 0.12 (0.54), residues: 93 loop : -0.82 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.012 0.001 TYR A 275 PHE 0.010 0.001 PHE A 218 TRP 0.007 0.001 TRP A 125 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3563) covalent geometry : angle 0.60242 ( 4872) hydrogen bonds : bond 0.03725 ( 187) hydrogen bonds : angle 4.36592 ( 549) Misc. bond : bond 0.13014 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7436 (p0) REVERT: A 320 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6307 (mpt-90) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 0.6576 time to fit residues: 35.8326 Evaluate side-chains 46 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.150300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121324 restraints weight = 3404.324| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.59 r_work: 0.3272 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 3565 Z= 0.109 Angle : 0.593 12.655 4872 Z= 0.256 Chirality : 0.039 0.144 509 Planarity : 0.003 0.024 580 Dihedral : 10.514 77.289 513 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.18 % Allowed : 26.01 % Favored : 70.81 % 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 aren not related in a simple way. whole: 1.12 (0.42), residues: 397 helix: 1.90 (0.36), residues: 201 sheet: 0.02 (0.54), residues: 93 loop : -0.81 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.012 0.001 TYR A 275 PHE 0.010 0.001 PHE A 218 TRP 0.007 0.001 TRP A 125 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3563) covalent geometry : angle 0.59339 ( 4872) hydrogen bonds : bond 0.03497 ( 187) hydrogen bonds : angle 4.22594 ( 549) Misc. bond : bond 0.12205 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7327 (p0) REVERT: A 318 SER cc_start: 0.7110 (t) cc_final: 0.6891 (p) REVERT: A 320 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6280 (mpt-90) outliers start: 11 outliers final: 4 residues processed: 56 average time/residue: 0.6012 time to fit residues: 34.6704 Evaluate side-chains 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.149594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120411 restraints weight = 3464.290| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.60 r_work: 0.3255 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 3565 Z= 0.122 Angle : 0.616 12.920 4872 Z= 0.263 Chirality : 0.040 0.146 509 Planarity : 0.003 0.022 580 Dihedral : 10.583 77.646 513 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.60 % Allowed : 26.59 % Favored : 70.81 % 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 aren not related in a simple way. whole: 1.07 (0.42), residues: 397 helix: 1.86 (0.36), residues: 201 sheet: 0.01 (0.54), residues: 93 loop : -0.84 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.012 0.001 TYR A 275 PHE 0.009 0.001 PHE A 218 TRP 0.006 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3563) covalent geometry : angle 0.61604 ( 4872) hydrogen bonds : bond 0.03649 ( 187) hydrogen bonds : angle 4.23429 ( 549) Misc. bond : bond 0.13293 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7309 (p0) REVERT: A 318 SER cc_start: 0.7165 (t) cc_final: 0.6891 (p) REVERT: A 320 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6297 (mpt-90) outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 0.5485 time to fit residues: 29.9968 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.0050 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.149550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120449 restraints weight = 3427.280| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.59 r_work: 0.3250 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 3565 Z= 0.122 Angle : 0.620 12.931 4872 Z= 0.264 Chirality : 0.040 0.145 509 Planarity : 0.003 0.021 580 Dihedral : 10.564 77.533 513 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.60 % Allowed : 26.88 % Favored : 70.52 % 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 aren not related in a simple way. whole: 1.07 (0.42), residues: 397 helix: 1.86 (0.36), residues: 201 sheet: 0.00 (0.54), residues: 93 loop : -0.84 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.012 0.001 TYR A 275 PHE 0.010 0.001 PHE A 218 TRP 0.006 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3563) covalent geometry : angle 0.62034 ( 4872) hydrogen bonds : bond 0.03626 ( 187) hydrogen bonds : angle 4.21036 ( 549) Misc. bond : bond 0.13146 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7286 (p0) REVERT: A 318 SER cc_start: 0.7142 (t) cc_final: 0.6885 (p) REVERT: A 320 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6142 (mpt-90) outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 0.5983 time to fit residues: 32.6609 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.0060 chunk 2 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.150381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121154 restraints weight = 3488.932| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.61 r_work: 0.3269 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 3565 Z= 0.111 Angle : 0.613 12.621 4872 Z= 0.259 Chirality : 0.040 0.154 509 Planarity : 0.003 0.021 580 Dihedral : 10.306 77.423 513 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.31 % Allowed : 27.17 % Favored : 70.52 % 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 aren not related in a simple way. whole: 1.10 (0.42), residues: 397 helix: 1.90 (0.36), residues: 202 sheet: -0.04 (0.53), residues: 93 loop : -0.82 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.012 0.001 TYR A 275 PHE 0.010 0.001 PHE A 218 TRP 0.007 0.001 TRP A 125 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3563) covalent geometry : angle 0.61274 ( 4872) hydrogen bonds : bond 0.03423 ( 187) hydrogen bonds : angle 4.14867 ( 549) Misc. bond : bond 0.11946 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7232 (p0) REVERT: A 318 SER cc_start: 0.7195 (t) cc_final: 0.6962 (p) outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 0.5782 time to fit residues: 32.1302 Evaluate side-chains 49 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.150368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121117 restraints weight = 3481.228| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.61 r_work: 0.3265 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 3565 Z= 0.116 Angle : 0.623 12.727 4872 Z= 0.263 Chirality : 0.040 0.155 509 Planarity : 0.003 0.021 580 Dihedral : 10.238 77.656 513 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.02 % Allowed : 27.46 % Favored : 70.52 % 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 aren not related in a simple way. whole: 1.07 (0.42), residues: 397 helix: 1.88 (0.36), residues: 202 sheet: -0.09 (0.53), residues: 93 loop : -0.81 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.012 0.001 TYR A 275 PHE 0.010 0.001 PHE A 218 TRP 0.006 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3563) covalent geometry : angle 0.62290 ( 4872) hydrogen bonds : bond 0.03500 ( 187) hydrogen bonds : angle 4.15705 ( 549) Misc. bond : bond 0.12258 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7367 (p0) REVERT: A 318 SER cc_start: 0.7244 (t) cc_final: 0.6983 (p) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.5703 time to fit residues: 30.0358 Evaluate side-chains 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.148687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119465 restraints weight = 3411.036| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.58 r_work: 0.3246 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 3565 Z= 0.140 Angle : 0.654 13.285 4872 Z= 0.277 Chirality : 0.042 0.156 509 Planarity : 0.003 0.021 580 Dihedral : 10.527 77.490 513 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.02 % Allowed : 27.17 % Favored : 70.81 % 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 aren not related in a simple way. whole: 0.92 (0.42), residues: 397 helix: 1.77 (0.36), residues: 201 sheet: -0.09 (0.53), residues: 93 loop : -0.93 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.012 0.002 TYR A 275 PHE 0.010 0.001 PHE A 218 TRP 0.006 0.001 TRP A 125 HIS 0.007 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3563) covalent geometry : angle 0.65446 ( 4872) hydrogen bonds : bond 0.03828 ( 187) hydrogen bonds : angle 4.25499 ( 549) Misc. bond : bond 0.15240 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7424 (p0) REVERT: A 318 SER cc_start: 0.7305 (t) cc_final: 0.6991 (p) REVERT: A 394 TYR cc_start: 0.6737 (p90) cc_final: 0.6187 (p90) outliers start: 7 outliers final: 6 residues processed: 53 average time/residue: 0.5742 time to fit residues: 31.4269 Evaluate side-chains 52 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.150344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121178 restraints weight = 3484.716| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.59 r_work: 0.3265 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 3565 Z= 0.114 Angle : 0.629 12.810 4872 Z= 0.265 Chirality : 0.040 0.162 509 Planarity : 0.003 0.022 580 Dihedral : 10.176 76.899 513 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.02 % Allowed : 27.17 % Favored : 70.81 % 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 aren not related in a simple way. whole: 1.01 (0.42), residues: 397 helix: 1.88 (0.36), residues: 201 sheet: -0.12 (0.53), residues: 93 loop : -0.90 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.012 0.001 TYR A 275 PHE 0.010 0.001 PHE A 218 TRP 0.007 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3563) covalent geometry : angle 0.62918 ( 4872) hydrogen bonds : bond 0.03473 ( 187) hydrogen bonds : angle 4.15891 ( 549) Misc. bond : bond 0.12280 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7345 (p0) REVERT: A 318 SER cc_start: 0.7265 (t) cc_final: 0.6994 (p) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.5767 time to fit residues: 30.9103 Evaluate side-chains 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.149833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120564 restraints weight = 3485.746| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.60 r_work: 0.3252 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 3565 Z= 0.122 Angle : 0.637 12.895 4872 Z= 0.268 Chirality : 0.041 0.161 509 Planarity : 0.003 0.021 580 Dihedral : 10.226 77.151 513 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.73 % Allowed : 27.75 % Favored : 70.52 % 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 aren not related in a simple way. whole: 0.98 (0.42), residues: 397 helix: 1.84 (0.36), residues: 201 sheet: -0.13 (0.53), residues: 93 loop : -0.91 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.012 0.001 TYR A 275 PHE 0.010 0.001 PHE A 218 TRP 0.007 0.001 TRP A 125 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3563) covalent geometry : angle 0.63716 ( 4872) hydrogen bonds : bond 0.03570 ( 187) hydrogen bonds : angle 4.17567 ( 549) Misc. bond : bond 0.12601 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1519.00 seconds wall clock time: 26 minutes 53.18 seconds (1613.18 seconds total)