Starting phenix.real_space_refine on Tue Aug 4 16:37:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ovm_70902/08_2026/9ovm_70902_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ovm_70902/08_2026/9ovm_70902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ovm_70902/08_2026/9ovm_70902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ovm_70902/08_2026/9ovm_70902.map" model { file = "/net/cci-nas-00/data/ceres_data/9ovm_70902/08_2026/9ovm_70902_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ovm_70902/08_2026/9ovm_70902_trim.cif" } resolution = 2.05 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= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 11 5.16 5 C 1564 2.51 5 N 373 2.21 5 O 490 1.98 5 H 2207 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4645 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4499 Classifications: {'peptide': 284} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 269} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 51 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2, 'water': 23} Link IDs: {None: 24} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.79, per 1000 atoms: 0.17 Number of scatterers: 4645 At special positions: 0 Unit cell: (71.688, 65.92, 73.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 490 8.00 N 373 7.00 C 1564 6.00 H 2207 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 174 " distance=2.02 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 202 " distance=2.05 Simple disulfide: pdb=" SG CYS A 181 " - pdb=" SG CYS A 261 " distance=2.02 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A1401 " - " ASN A 64 " " NAG A1402 " - " ASN A 213 " " NAG B 1 " - " ASN A 20 " " NAG C 1 " - " ASN A 138 " " NAG D 1 " - " ASN A 207 " Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 61.7 milliseconds 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 526 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 6 sheets defined 4.9% alpha, 46.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 94 through 97 removed outlier: 3.758A pdb=" N LYS A 97 " --> pdb=" O LEU A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 45 removed outlier: 8.377A pdb=" N THR A 79 " --> pdb=" O PRO A 277 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY A 107 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N PHE A 232 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE A 241 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 73 removed outlier: 3.685A pdb=" N ASN A 295 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 87 removed outlier: 8.455A pdb=" N THR A 260 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR A 179 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP A 193 " --> pdb=" O CYS A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 102 through 103 removed outlier: 3.858A pdb=" N GLY A 162 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 119 85 hydrogen bonds defined for protein. 216 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: 0.80 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 2207 1.11 - 1.29: 364 1.29 - 1.46: 970 1.46 - 1.64: 1134 1.64 - 1.81: 16 Bond restraints: 4691 Sorted by residual: bond pdb=" ND2 ASN A 138 " pdb="HD21 ASN A 138 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN A 64 " pdb="HD21 ASN A 64 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CE2 TYR A 218 " pdb=" HE2 TYR A 218 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CZ PHE A 241 " pdb=" HZ PHE A 241 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CE1 PHE A 237 " pdb=" HE1 PHE A 237 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 4686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 6612 1.77 - 3.55: 1094 3.55 - 5.32: 422 5.32 - 7.09: 226 7.09 - 8.87: 15 Bond angle restraints: 8369 Sorted by residual: angle pdb=" CB HIS A 253 " pdb=" CG HIS A 253 " pdb=" CD2 HIS A 253 " ideal model delta sigma weight residual 131.20 124.49 6.71 1.30e+00 5.92e-01 2.66e+01 angle pdb=" N PRO A 38 " pdb=" CA PRO A 38 " pdb=" CB PRO A 38 " ideal model delta sigma weight residual 103.22 105.70 -2.48 5.20e-01 3.70e+00 2.27e+01 angle pdb=" C THR A 276 " pdb=" CA THR A 276 " pdb=" CB THR A 276 " ideal model delta sigma weight residual 109.20 116.29 -7.09 1.50e+00 4.44e-01 2.23e+01 angle pdb=" CA PHE A 208 " pdb=" C PHE A 208 " pdb=" N THR A 209 " ideal model delta sigma weight residual 116.29 122.39 -6.10 1.30e+00 5.92e-01 2.20e+01 angle pdb=" CB HIS A 220 " pdb=" CG HIS A 220 " pdb=" CD2 HIS A 220 " ideal model delta sigma weight residual 131.20 125.33 5.87 1.30e+00 5.92e-01 2.04e+01 ... (remaining 8364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 2178 21.04 - 42.08: 118 42.08 - 63.12: 68 63.12 - 84.16: 18 84.16 - 105.20: 8 Dihedral angle restraints: 2390 sinusoidal: 1325 harmonic: 1065 Sorted by residual: dihedral pdb=" CA THR A 79 " pdb=" C THR A 79 " pdb=" N TYR A 80 " pdb=" CA TYR A 80 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA PHE A 232 " pdb=" C PHE A 232 " pdb=" N THR A 233 " pdb=" CA THR A 233 " ideal model delta harmonic sigma weight residual 180.00 152.39 27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ASN A 138 " pdb=" C ASN A 138 " pdb=" N THR A 139 " pdb=" CA THR A 139 " ideal model delta harmonic sigma weight residual -180.00 -153.55 -26.45 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 2387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 161 0.059 - 0.118: 138 0.118 - 0.177: 80 0.177 - 0.236: 10 0.236 - 0.295: 10 Chirality restraints: 399 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.22e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.63e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.42e+01 ... (remaining 396 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1401 " 0.158 2.00e-02 2.50e+03 1.31e-01 2.16e+02 pdb=" C7 NAG A1401 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A1401 " 0.117 2.00e-02 2.50e+03 pdb=" N2 NAG A1401 " -0.212 2.00e-02 2.50e+03 pdb=" O7 NAG A1401 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " -0.140 2.00e-02 2.50e+03 1.06e-01 1.70e+02 pdb=" CG ASN A 138 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " 0.096 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " 0.022 2.00e-02 2.50e+03 pdb="HD21 ASN A 138 " 0.131 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 207 " 0.126 2.00e-02 2.50e+03 9.99e-02 1.50e+02 pdb=" CG ASN A 207 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 207 " -0.098 2.00e-02 2.50e+03 pdb=" ND2 ASN A 207 " -0.018 2.00e-02 2.50e+03 pdb="HD21 ASN A 207 " -0.127 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.132 2.00e-02 2.50e+03 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 498 2.24 - 2.83: 8905 2.83 - 3.42: 12430 3.42 - 4.01: 17400 4.01 - 4.60: 25109 Nonbonded interactions: 64342 Sorted by model distance: nonbonded pdb=" OD2 ASP A 35 " pdb=" HG SER A 92 " model vdw 1.649 2.450 nonbonded pdb=" H THR A 36 " pdb=" H GLY A 37 " model vdw 1.662 2.100 nonbonded pdb="HD21 ASN A 114 " pdb=" O ALA A 214 " model vdw 1.682 2.450 nonbonded pdb=" O TRP A 95 " pdb=" HH TYR A 255 " model vdw 1.683 2.450 nonbonded pdb=" OD1 ASN A 114 " pdb=" HG SER A 125 " model vdw 1.720 2.450 ... (remaining 64337 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 5.450 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: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.030 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 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 : 0.014 0.071 2496 Z= 0.797 Angle : 1.726 7.942 3421 Z= 1.114 Chirality : 0.100 0.295 399 Planarity : 0.014 0.131 416 Dihedral : 14.163 105.198 1013 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.48), residues: 282 helix: None (None), residues: 0 sheet: 0.30 (0.47), residues: 104 loop : -0.63 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 60 TYR 0.080 0.018 TYR A 56 PHE 0.036 0.012 PHE A 109 TRP 0.041 0.016 TRP A 274 HIS 0.009 0.004 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.01387 / 0.80 ( 2484) covalent geometry : angle 1.69477 / 1.11 ( 3388) SS BOND : bond 0.01143 / 0.53 ( 3) SS BOND : angle 2.40573 / 1.17 ( 6) hydrogen bonds : bond 0.14442 / 9.09 ( 85) hydrogen bonds : angle 8.51647 / 5.87 ( 216) link_BETA1-4 : bond 0.02237 / 1.07 ( 4) link_BETA1-4 : angle 3.59969 / 2.08 ( 12) link_NAG-ASN : bond 0.01095 / 0.58 ( 5) link_NAG-ASN : angle 4.21427 / 2.45 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 LYS cc_start: 0.8992 (mttm) cc_final: 0.8122 (mmtt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 1.3608 time to fit residues: 67.8244 Evaluate side-chains 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.062321 restraints weight = 11496.901| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.56 r_work: 0.2807 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 2496 Z= 0.198 Angle : 0.735 7.746 3421 Z= 0.381 Chirality : 0.046 0.166 399 Planarity : 0.005 0.063 416 Dihedral : 11.173 69.198 502 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.78 % Allowed : 8.24 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.49), residues: 282 helix: None (None), residues: 0 sheet: -0.01 (0.48), residues: 108 loop : -0.32 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 26 TYR 0.025 0.002 TYR A 80 PHE 0.009 0.002 PHE A 219 TRP 0.012 0.002 TRP A 193 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 2484) covalent geometry : angle 0.69959 / 0.37 ( 3388) SS BOND : bond 0.00113 / 0.05 ( 3) SS BOND : angle 3.27243 / 1.91 ( 6) hydrogen bonds : bond 0.05329 / 3.41 ( 85) hydrogen bonds : angle 7.57822 / 5.09 ( 216) link_BETA1-4 : bond 0.00269 / 0.13 ( 4) link_BETA1-4 : angle 2.23438 / 1.17 ( 12) link_NAG-ASN : bond 0.00224 / 0.13 ( 5) link_NAG-ASN : angle 2.09390 / 1.08 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.154 Fit side-chains REVERT: A 272 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9053 (mt-10) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 1.0551 time to fit residues: 37.8016 Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 1 optimal weight: 0.0000 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.062920 restraints weight = 11491.817| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.46 r_work: 0.2823 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 2496 Z= 0.159 Angle : 0.683 11.686 3421 Z= 0.350 Chirality : 0.046 0.196 399 Planarity : 0.005 0.040 416 Dihedral : 8.474 54.410 502 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.78 % Allowed : 9.41 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.50), residues: 282 helix: None (None), residues: 0 sheet: -0.08 (0.48), residues: 106 loop : -0.16 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 26 TYR 0.022 0.001 TYR A 80 PHE 0.011 0.001 PHE A 127 TRP 0.008 0.001 TRP A 193 HIS 0.002 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 2484) covalent geometry : angle 0.63500 / 0.33 ( 3388) SS BOND : bond 0.00207 / 0.10 ( 3) SS BOND : angle 4.92780 / 2.86 ( 6) hydrogen bonds : bond 0.04486 / 2.89 ( 85) hydrogen bonds : angle 7.25920 / 4.86 ( 216) link_BETA1-4 : bond 0.00303 / 0.15 ( 4) link_BETA1-4 : angle 1.70752 / 0.88 ( 12) link_NAG-ASN : bond 0.00115 / 0.06 ( 5) link_NAG-ASN : angle 1.78318 / 0.92 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.134 Fit side-chains REVERT: A 26 ARG cc_start: 0.8787 (mpp80) cc_final: 0.8546 (mtm-85) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 1.2083 time to fit residues: 34.6516 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.062620 restraints weight = 11431.929| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.52 r_work: 0.2813 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 2496 Z= 0.163 Angle : 0.623 10.484 3421 Z= 0.323 Chirality : 0.044 0.171 399 Planarity : 0.005 0.048 416 Dihedral : 6.259 49.589 502 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.18 % Allowed : 9.02 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.49), residues: 282 helix: None (None), residues: 0 sheet: -0.07 (0.46), residues: 107 loop : 0.08 (0.49), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.023 0.001 TYR A 80 PHE 0.011 0.001 PHE A 127 TRP 0.008 0.001 TRP A 193 HIS 0.002 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 2484) covalent geometry : angle 0.57984 / 0.31 ( 3388) SS BOND : bond 0.00550 / 0.26 ( 3) SS BOND : angle 4.55094 / 2.61 ( 6) hydrogen bonds : bond 0.04170 / 2.71 ( 85) hydrogen bonds : angle 7.07154 / 4.67 ( 216) link_BETA1-4 : bond 0.00294 / 0.15 ( 4) link_BETA1-4 : angle 1.40741 / 0.73 ( 12) link_NAG-ASN : bond 0.00084 / 0.05 ( 5) link_NAG-ASN : angle 1.60902 / 0.83 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8833 (mpp80) cc_final: 0.8595 (mtm-85) outliers start: 3 outliers final: 2 residues processed: 29 average time/residue: 1.3645 time to fit residues: 40.4476 Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 24 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.062084 restraints weight = 11403.668| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.50 r_work: 0.2805 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 2496 Z= 0.175 Angle : 0.603 9.647 3421 Z= 0.315 Chirality : 0.044 0.169 399 Planarity : 0.004 0.045 416 Dihedral : 5.710 44.966 502 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.78 % Allowed : 9.80 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.49), residues: 282 helix: None (None), residues: 0 sheet: -0.24 (0.44), residues: 111 loop : 0.18 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.020 0.001 TYR A 80 PHE 0.010 0.001 PHE A 221 TRP 0.007 0.001 TRP A 193 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 2484) covalent geometry : angle 0.56623 / 0.30 ( 3388) SS BOND : bond 0.00455 / 0.22 ( 3) SS BOND : angle 4.08664 / 2.37 ( 6) hydrogen bonds : bond 0.04174 / 2.70 ( 85) hydrogen bonds : angle 6.98783 / 4.62 ( 216) link_BETA1-4 : bond 0.00209 / 0.10 ( 4) link_BETA1-4 : angle 1.32563 / 0.70 ( 12) link_NAG-ASN : bond 0.00119 / 0.07 ( 5) link_NAG-ASN : angle 1.57542 / 0.83 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.132 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 1.2990 time to fit residues: 39.8445 Evaluate side-chains 31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062639 restraints weight = 11573.633| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.52 r_work: 0.2815 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 2496 Z= 0.149 Angle : 0.594 9.423 3421 Z= 0.310 Chirality : 0.044 0.163 399 Planarity : 0.005 0.051 416 Dihedral : 5.429 42.038 502 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.78 % Allowed : 9.80 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.49), residues: 282 helix: None (None), residues: 0 sheet: -0.24 (0.44), residues: 111 loop : 0.24 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.019 0.001 TYR A 80 PHE 0.010 0.001 PHE A 127 TRP 0.007 0.001 TRP A 193 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 2484) covalent geometry : angle 0.55845 / 0.30 ( 3388) SS BOND : bond 0.00433 / 0.21 ( 3) SS BOND : angle 3.98634 / 2.31 ( 6) hydrogen bonds : bond 0.03981 / 2.60 ( 85) hydrogen bonds : angle 6.95170 / 4.57 ( 216) link_BETA1-4 : bond 0.00253 / 0.12 ( 4) link_BETA1-4 : angle 1.29949 / 0.69 ( 12) link_NAG-ASN : bond 0.00086 / 0.06 ( 5) link_NAG-ASN : angle 1.52363 / 0.79 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.158 Fit side-chains REVERT: A 159 LYS cc_start: 0.8723 (ptmt) cc_final: 0.8516 (ptmm) outliers start: 2 outliers final: 2 residues processed: 31 average time/residue: 1.2754 time to fit residues: 40.4404 Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.062391 restraints weight = 11365.124| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.48 r_work: 0.2814 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 2496 Z= 0.158 Angle : 0.596 9.337 3421 Z= 0.311 Chirality : 0.044 0.163 399 Planarity : 0.005 0.051 416 Dihedral : 5.167 39.725 502 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.78 % Allowed : 10.98 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.50), residues: 282 helix: None (None), residues: 0 sheet: -0.22 (0.45), residues: 111 loop : 0.32 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 34 TYR 0.019 0.001 TYR A 80 PHE 0.009 0.001 PHE A 127 TRP 0.006 0.001 TRP A 193 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 2484) covalent geometry : angle 0.56216 / 0.30 ( 3388) SS BOND : bond 0.00429 / 0.20 ( 3) SS BOND : angle 3.94935 / 2.29 ( 6) hydrogen bonds : bond 0.04018 / 2.62 ( 85) hydrogen bonds : angle 6.87572 / 4.53 ( 216) link_BETA1-4 : bond 0.00230 / 0.11 ( 4) link_BETA1-4 : angle 1.27401 / 0.67 ( 12) link_NAG-ASN : bond 0.00106 / 0.07 ( 5) link_NAG-ASN : angle 1.48785 / 0.77 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.134 Fit side-chains REVERT: A 159 LYS cc_start: 0.8717 (ptmt) cc_final: 0.8510 (ptmm) outliers start: 2 outliers final: 2 residues processed: 31 average time/residue: 1.2670 time to fit residues: 40.1752 Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.083797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.061812 restraints weight = 11528.080| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.47 r_work: 0.2797 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 2496 Z= 0.184 Angle : 0.615 9.392 3421 Z= 0.321 Chirality : 0.045 0.170 399 Planarity : 0.005 0.054 416 Dihedral : 5.098 38.035 502 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.78 % Allowed : 11.37 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.49), residues: 282 helix: None (None), residues: 0 sheet: -0.22 (0.44), residues: 111 loop : 0.23 (0.49), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 34 TYR 0.019 0.001 TYR A 80 PHE 0.010 0.001 PHE A 221 TRP 0.006 0.001 TRP A 193 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 2484) covalent geometry : angle 0.58072 / 0.31 ( 3388) SS BOND : bond 0.00443 / 0.21 ( 3) SS BOND : angle 3.96567 / 2.30 ( 6) hydrogen bonds : bond 0.04079 / 2.66 ( 85) hydrogen bonds : angle 6.89880 / 4.54 ( 216) link_BETA1-4 : bond 0.00222 / 0.11 ( 4) link_BETA1-4 : angle 1.30860 / 0.69 ( 12) link_NAG-ASN : bond 0.00177 / 0.09 ( 5) link_NAG-ASN : angle 1.60236 / 0.84 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.135 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 1.3478 time to fit residues: 41.3319 Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 2 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.084266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.062270 restraints weight = 11247.913| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.51 r_work: 0.2813 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 2496 Z= 0.170 Angle : 0.609 9.315 3421 Z= 0.318 Chirality : 0.045 0.166 399 Planarity : 0.005 0.054 416 Dihedral : 4.976 36.405 502 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.78 % Allowed : 11.76 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.49), residues: 282 helix: None (None), residues: 0 sheet: -0.19 (0.44), residues: 111 loop : 0.20 (0.49), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 34 TYR 0.017 0.001 TYR A 80 PHE 0.010 0.001 PHE A 221 TRP 0.006 0.001 TRP A 193 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 2484) covalent geometry : angle 0.57570 / 0.31 ( 3388) SS BOND : bond 0.00428 / 0.20 ( 3) SS BOND : angle 3.92349 / 2.28 ( 6) hydrogen bonds : bond 0.03912 / 2.54 ( 85) hydrogen bonds : angle 6.75106 / 4.45 ( 216) link_BETA1-4 : bond 0.00170 / 0.08 ( 4) link_BETA1-4 : angle 1.23188 / 0.65 ( 12) link_NAG-ASN : bond 0.00116 / 0.06 ( 5) link_NAG-ASN : angle 1.50895 / 0.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.136 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 1.2611 time to fit residues: 41.2538 Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.063528 restraints weight = 11370.734| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.49 r_work: 0.2840 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 2496 Z= 0.146 Angle : 0.611 9.179 3421 Z= 0.320 Chirality : 0.045 0.158 399 Planarity : 0.005 0.056 416 Dihedral : 4.853 35.430 502 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.78 % Allowed : 12.94 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.49), residues: 282 helix: None (None), residues: 0 sheet: -0.15 (0.45), residues: 111 loop : 0.22 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 34 TYR 0.017 0.001 TYR A 80 PHE 0.009 0.001 PHE A 127 TRP 0.007 0.001 TRP A 193 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 2484) covalent geometry : angle 0.57917 / 0.31 ( 3388) SS BOND : bond 0.00406 / 0.19 ( 3) SS BOND : angle 3.86177 / 2.24 ( 6) hydrogen bonds : bond 0.03673 / 2.39 ( 85) hydrogen bonds : angle 6.66740 / 4.39 ( 216) link_BETA1-4 : bond 0.00246 / 0.12 ( 4) link_BETA1-4 : angle 1.23762 / 0.66 ( 12) link_NAG-ASN : bond 0.00095 / 0.06 ( 5) link_NAG-ASN : angle 1.48757 / 0.76 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.133 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 1.4509 time to fit residues: 47.4508 Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 4 optimal weight: 0.0870 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.064229 restraints weight = 11354.152| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.50 r_work: 0.2856 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 2496 Z= 0.138 Angle : 0.600 9.080 3421 Z= 0.315 Chirality : 0.045 0.154 399 Planarity : 0.006 0.085 416 Dihedral : 4.777 34.732 502 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.78 % Allowed : 12.16 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.49), residues: 282 helix: None (None), residues: 0 sheet: -0.08 (0.44), residues: 113 loop : 0.21 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 34 TYR 0.016 0.001 TYR A 80 PHE 0.008 0.001 PHE A 127 TRP 0.007 0.001 TRP A 193 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 2484) covalent geometry : angle 0.56858 / 0.30 ( 3388) SS BOND : bond 0.00409 / 0.19 ( 3) SS BOND : angle 3.82455 / 2.22 ( 6) hydrogen bonds : bond 0.03613 / 2.34 ( 85) hydrogen bonds : angle 6.57946 / 4.34 ( 216) link_BETA1-4 : bond 0.00270 / 0.13 ( 4) link_BETA1-4 : angle 1.22123 / 0.65 ( 12) link_NAG-ASN : bond 0.00095 / 0.06 ( 5) link_NAG-ASN : angle 1.46092 / 0.75 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3307.71 seconds wall clock time: 56 minutes 45.65 seconds (3405.65 seconds total)