Starting phenix.real_space_refine on Tue Mar 3 12:42:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uaq_26430/03_2026/7uaq_26430.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uaq_26430/03_2026/7uaq_26430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uaq_26430/03_2026/7uaq_26430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uaq_26430/03_2026/7uaq_26430.map" model { file = "/net/cci-nas-00/data/ceres_data/7uaq_26430/03_2026/7uaq_26430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uaq_26430/03_2026/7uaq_26430.cif" } resolution = 3.1 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= -0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2773 2.51 5 N 723 2.21 5 O 850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4362 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2392 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain breaks: 2 Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 833 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.20, per 1000 atoms: 0.28 Number of scatterers: 4362 At special positions: 0 Unit cell: (96.82, 64.89, 89.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 850 8.00 N 723 7.00 C 2773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " " NAG C 1 " - " ASN A 149 " " NAG D 1 " - " ASN A 234 " " NAG L 301 " - " ASN L 20 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 178.2 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 12 sheets defined 4.9% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.625A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 29 removed outlier: 3.625A pdb=" N ASN L 29 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.628A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.319A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.501A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.301A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.693A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 7 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 34 through 39 removed outlier: 7.162A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89 removed outlier: 3.612A pdb=" N ALA H 88 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.936A pdb=" N ILE H 112 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.524A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 44 through 50 removed outlier: 6.653A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) 91 hydrogen bonds defined for protein. 231 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: 0.48 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1293 1.34 - 1.46: 1224 1.46 - 1.59: 1933 1.59 - 1.72: 0 1.72 - 1.84: 22 Bond restraints: 4472 Sorted by residual: bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" N ILE A 197 " pdb=" CA ILE A 197 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.18e-02 7.18e+03 8.87e+00 bond pdb=" N ILE A 68 " pdb=" CA ILE A 68 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.85e+00 bond pdb=" N GLY L 101 " pdb=" CA GLY L 101 " ideal model delta sigma weight residual 1.447 1.474 -0.027 1.09e-02 8.42e+03 6.11e+00 ... (remaining 4467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 5766 2.49 - 4.99: 266 4.99 - 7.48: 28 7.48 - 9.98: 11 9.98 - 12.47: 2 Bond angle restraints: 6073 Sorted by residual: angle pdb=" C ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta sigma weight residual 110.42 122.89 -12.47 1.99e+00 2.53e-01 3.93e+01 angle pdb=" N ASN A 122 " pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " ideal model delta sigma weight residual 110.45 101.66 8.79 1.44e+00 4.82e-01 3.73e+01 angle pdb=" CA GLY L 101 " pdb=" C GLY L 101 " pdb=" O GLY L 101 " ideal model delta sigma weight residual 122.29 117.98 4.31 8.10e-01 1.52e+00 2.83e+01 angle pdb=" N ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta sigma weight residual 110.49 101.68 8.81 1.69e+00 3.50e-01 2.72e+01 angle pdb=" N ASN L 20 " pdb=" CA ASN L 20 " pdb=" CB ASN L 20 " ideal model delta sigma weight residual 110.84 104.20 6.64 1.52e+00 4.33e-01 1.91e+01 ... (remaining 6068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 2435 14.78 - 29.56: 219 29.56 - 44.34: 53 44.34 - 59.13: 28 59.13 - 73.91: 4 Dihedral angle restraints: 2739 sinusoidal: 1197 harmonic: 1542 Sorted by residual: dihedral pdb=" N ASN A 122 " pdb=" C ASN A 122 " pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " ideal model delta harmonic sigma weight residual 122.80 110.48 12.32 0 2.50e+00 1.60e-01 2.43e+01 dihedral pdb=" CA GLN H 81 " pdb=" C GLN H 81 " pdb=" N MET H 82 " pdb=" CA MET H 82 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA HIS L 54B" pdb=" C HIS L 54B" pdb=" N THR L 54C" pdb=" CA THR L 54C" ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 2736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 537 0.078 - 0.155: 128 0.155 - 0.233: 15 0.233 - 0.310: 3 0.310 - 0.388: 4 Chirality restraints: 687 Sorted by residual: chirality pdb=" C4 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O4 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.14 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 684 not shown) Planarity restraints: 773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.010 2.00e-02 2.50e+03 7.50e-02 7.02e+01 pdb=" CG ASN A 165 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 224 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.64e+01 pdb=" N PRO A 225 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO A 225 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 225 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" CG ASN A 165 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.026 2.00e-02 2.50e+03 ... (remaining 770 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 125 2.66 - 3.22: 4192 3.22 - 3.78: 6567 3.78 - 4.34: 9038 4.34 - 4.90: 14761 Nonbonded interactions: 34683 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 102 " model vdw 2.101 3.040 nonbonded pdb=" OG1 THR L 22 " pdb=" OE2 GLU L 70 " model vdw 2.102 3.040 nonbonded pdb=" OE2 GLU A 96 " pdb=" N ASN A 99 " model vdw 2.158 3.120 nonbonded pdb=" O SER H 30 " pdb=" OG1 THR H 52A" model vdw 2.174 3.040 nonbonded pdb=" OE1 GLN A 14 " pdb=" NH1 ARG A 158 " model vdw 2.210 3.120 ... (remaining 34678 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' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 : 0.006 0.061 4487 Z= 0.326 Angle : 1.297 20.097 6113 Z= 0.686 Chirality : 0.071 0.388 687 Planarity : 0.008 0.129 766 Dihedral : 13.129 73.906 1740 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 0.22 % Allowed : 0.86 % Favored : 98.92 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.35), residues: 523 helix: -0.03 (1.56), residues: 11 sheet: -0.76 (0.46), residues: 139 loop : -2.30 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 319 TYR 0.032 0.002 TYR A 144 PHE 0.032 0.003 PHE L 72 TRP 0.020 0.002 TRP A 152 HIS 0.008 0.002 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 4472) covalent geometry : angle 1.18662 ( 6073) SS BOND : bond 0.00625 ( 5) SS BOND : angle 3.78987 ( 10) hydrogen bonds : bond 0.28573 ( 89) hydrogen bonds : angle 10.97881 ( 231) link_BETA1-4 : bond 0.00514 ( 3) link_BETA1-4 : angle 1.66685 ( 9) link_NAG-ASN : bond 0.01575 ( 7) link_NAG-ASN : angle 8.64520 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 158 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.8067 (mtt-85) REVERT: A 211 ASN cc_start: 0.8320 (p0) cc_final: 0.8032 (p0) REVERT: A 314 GLN cc_start: 0.6398 (tp40) cc_final: 0.6067 (tp40) REVERT: H 38 ARG cc_start: 0.6298 (ttm-80) cc_final: 0.6051 (ttm-80) REVERT: H 67 PHE cc_start: 0.7819 (m-80) cc_final: 0.7310 (m-80) REVERT: H 97 TYR cc_start: 0.7891 (t80) cc_final: 0.7566 (t80) REVERT: L 72 PHE cc_start: 0.7263 (m-10) cc_final: 0.6951 (m-80) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.0692 time to fit residues: 11.7414 Evaluate side-chains 87 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.118377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.094444 restraints weight = 10930.057| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 5.01 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4487 Z= 0.182 Angle : 0.933 12.359 6113 Z= 0.453 Chirality : 0.054 0.336 687 Planarity : 0.006 0.063 766 Dihedral : 8.582 57.434 794 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 2.59 % Allowed : 12.96 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.34), residues: 523 helix: 0.86 (1.67), residues: 11 sheet: -0.66 (0.44), residues: 139 loop : -2.23 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 38 TYR 0.026 0.002 TYR H 50 PHE 0.024 0.002 PHE A 238 TRP 0.012 0.002 TRP H 113 HIS 0.007 0.002 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 4472) covalent geometry : angle 0.86389 ( 6073) SS BOND : bond 0.00643 ( 5) SS BOND : angle 2.30687 ( 10) hydrogen bonds : bond 0.04115 ( 89) hydrogen bonds : angle 6.98876 ( 231) link_BETA1-4 : bond 0.00495 ( 3) link_BETA1-4 : angle 1.34837 ( 9) link_NAG-ASN : bond 0.01343 ( 7) link_NAG-ASN : angle 5.82986 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 190 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7507 (mtt-85) REVERT: A 211 ASN cc_start: 0.8685 (p0) cc_final: 0.8448 (p0) REVERT: A 298 GLU cc_start: 0.6955 (pt0) cc_final: 0.6193 (pt0) REVERT: A 314 GLN cc_start: 0.6769 (tp40) cc_final: 0.6265 (tp40) REVERT: L 4 LEU cc_start: 0.7497 (pt) cc_final: 0.7109 (pt) REVERT: L 85 ASP cc_start: 0.7640 (m-30) cc_final: 0.7002 (m-30) outliers start: 12 outliers final: 9 residues processed: 104 average time/residue: 0.0779 time to fit residues: 10.0605 Evaluate side-chains 100 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 0.0270 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.115196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.090988 restraints weight = 10891.454| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 5.02 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4487 Z= 0.197 Angle : 0.848 12.540 6113 Z= 0.413 Chirality : 0.051 0.319 687 Planarity : 0.005 0.050 766 Dihedral : 7.885 56.947 792 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 3.89 % Allowed : 13.61 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.35), residues: 523 helix: 1.37 (1.83), residues: 11 sheet: -0.53 (0.43), residues: 145 loop : -2.15 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 103 TYR 0.021 0.002 TYR H 50 PHE 0.022 0.002 PHE A 238 TRP 0.011 0.002 TRP L 91 HIS 0.005 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 4472) covalent geometry : angle 0.77872 ( 6073) SS BOND : bond 0.00315 ( 5) SS BOND : angle 1.95468 ( 10) hydrogen bonds : bond 0.03508 ( 89) hydrogen bonds : angle 6.44495 ( 231) link_BETA1-4 : bond 0.00441 ( 3) link_BETA1-4 : angle 1.33753 ( 9) link_NAG-ASN : bond 0.01118 ( 7) link_NAG-ASN : angle 5.61255 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 132 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 153 MET cc_start: 0.7575 (ptt) cc_final: 0.7250 (ptt) REVERT: A 169 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 190 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.7474 (mtt-85) REVERT: A 314 GLN cc_start: 0.6941 (tp40) cc_final: 0.6661 (tp40) REVERT: L 4 LEU cc_start: 0.7574 (pt) cc_final: 0.7242 (pt) REVERT: L 42 LYS cc_start: 0.8502 (mppt) cc_final: 0.8036 (mmtm) REVERT: L 85 ASP cc_start: 0.7802 (m-30) cc_final: 0.7518 (m-30) outliers start: 18 outliers final: 12 residues processed: 103 average time/residue: 0.0780 time to fit residues: 9.9298 Evaluate side-chains 99 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.114778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.090561 restraints weight = 10680.830| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 5.02 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4487 Z= 0.154 Angle : 0.774 11.363 6113 Z= 0.376 Chirality : 0.050 0.328 687 Planarity : 0.005 0.049 766 Dihedral : 7.392 56.905 792 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.75 % Favored : 90.06 % Rotamer: Outliers : 4.75 % Allowed : 14.47 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.36), residues: 523 helix: 1.40 (1.85), residues: 11 sheet: -0.50 (0.44), residues: 147 loop : -2.01 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 103 TYR 0.021 0.002 TYR H 50 PHE 0.015 0.002 PHE A 238 TRP 0.014 0.002 TRP H 36 HIS 0.006 0.002 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4472) covalent geometry : angle 0.70753 ( 6073) SS BOND : bond 0.00314 ( 5) SS BOND : angle 1.63855 ( 10) hydrogen bonds : bond 0.03114 ( 89) hydrogen bonds : angle 6.21886 ( 231) link_BETA1-4 : bond 0.00557 ( 3) link_BETA1-4 : angle 1.25887 ( 9) link_NAG-ASN : bond 0.01058 ( 7) link_NAG-ASN : angle 5.26704 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8191 (tm-30) REVERT: A 132 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 190 ARG cc_start: 0.8016 (mtt-85) cc_final: 0.7532 (mtt-85) REVERT: A 294 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7890 (t0) REVERT: A 298 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6187 (pt0) REVERT: A 314 GLN cc_start: 0.6916 (tp40) cc_final: 0.6630 (tp40) REVERT: H 72 ASP cc_start: 0.7294 (p0) cc_final: 0.7001 (p0) REVERT: H 100 TYR cc_start: 0.9283 (m-80) cc_final: 0.9046 (m-80) REVERT: L 4 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7222 (pt) REVERT: L 42 LYS cc_start: 0.8523 (mppt) cc_final: 0.8030 (mmtm) REVERT: L 45 ARG cc_start: 0.7390 (mtm110) cc_final: 0.7131 (ttp-110) REVERT: L 70 GLU cc_start: 0.7952 (pp20) cc_final: 0.7510 (pp20) REVERT: L 72 PHE cc_start: 0.7491 (m-80) cc_final: 0.6979 (t80) REVERT: L 103 ARG cc_start: 0.8614 (mmm160) cc_final: 0.8258 (mmm160) outliers start: 22 outliers final: 14 residues processed: 103 average time/residue: 0.0804 time to fit residues: 10.3659 Evaluate side-chains 109 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.112304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.088017 restraints weight = 10858.842| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 5.00 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4487 Z= 0.188 Angle : 0.778 10.550 6113 Z= 0.378 Chirality : 0.049 0.298 687 Planarity : 0.005 0.047 766 Dihedral : 7.272 56.479 792 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.56 % Favored : 90.25 % Rotamer: Outliers : 4.54 % Allowed : 16.85 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.36), residues: 523 helix: 1.50 (1.86), residues: 11 sheet: -0.58 (0.44), residues: 147 loop : -1.95 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.019 0.002 TYR H 108 PHE 0.012 0.002 PHE A 238 TRP 0.012 0.001 TRP A 258 HIS 0.005 0.001 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 4472) covalent geometry : angle 0.71322 ( 6073) SS BOND : bond 0.00240 ( 5) SS BOND : angle 1.86341 ( 10) hydrogen bonds : bond 0.03072 ( 89) hydrogen bonds : angle 6.17890 ( 231) link_BETA1-4 : bond 0.00398 ( 3) link_BETA1-4 : angle 1.24205 ( 9) link_NAG-ASN : bond 0.01011 ( 7) link_NAG-ASN : angle 5.17093 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 69 HIS cc_start: 0.8162 (t-90) cc_final: 0.7907 (t-90) REVERT: A 115 GLN cc_start: 0.8743 (mm110) cc_final: 0.8504 (mm-40) REVERT: A 190 ARG cc_start: 0.7936 (mtt-85) cc_final: 0.7608 (mtt-85) REVERT: A 314 GLN cc_start: 0.7116 (tp40) cc_final: 0.6796 (tp40) REVERT: L 4 LEU cc_start: 0.7659 (pt) cc_final: 0.7357 (pt) REVERT: L 45 ARG cc_start: 0.7437 (mtm110) cc_final: 0.7161 (ttp-110) REVERT: L 70 GLU cc_start: 0.7908 (pp20) cc_final: 0.7424 (pp20) REVERT: L 72 PHE cc_start: 0.7475 (m-80) cc_final: 0.6845 (t80) REVERT: L 85 ASP cc_start: 0.7884 (m-30) cc_final: 0.7505 (m-30) REVERT: L 103 ARG cc_start: 0.8632 (mmm160) cc_final: 0.8116 (mmm160) outliers start: 21 outliers final: 18 residues processed: 104 average time/residue: 0.0749 time to fit residues: 9.7730 Evaluate side-chains 109 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 0.0270 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.113047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.088626 restraints weight = 11000.037| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 5.07 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4487 Z= 0.154 Angle : 0.752 10.456 6113 Z= 0.364 Chirality : 0.049 0.341 687 Planarity : 0.005 0.048 766 Dihedral : 7.166 56.434 792 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.56 % Favored : 90.25 % Rotamer: Outliers : 5.18 % Allowed : 16.41 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.36), residues: 523 helix: 1.52 (1.88), residues: 11 sheet: -0.61 (0.45), residues: 147 loop : -1.93 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 38 TYR 0.019 0.002 TYR H 50 PHE 0.011 0.001 PHE A 238 TRP 0.013 0.001 TRP H 36 HIS 0.006 0.001 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4472) covalent geometry : angle 0.69061 ( 6073) SS BOND : bond 0.00205 ( 5) SS BOND : angle 1.36057 ( 10) hydrogen bonds : bond 0.02916 ( 89) hydrogen bonds : angle 6.09197 ( 231) link_BETA1-4 : bond 0.00516 ( 3) link_BETA1-4 : angle 1.21542 ( 9) link_NAG-ASN : bond 0.01009 ( 7) link_NAG-ASN : angle 5.00327 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 115 GLN cc_start: 0.8817 (mm110) cc_final: 0.8579 (mm-40) REVERT: A 132 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 190 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7610 (mtt-85) REVERT: A 314 GLN cc_start: 0.7084 (tp40) cc_final: 0.6804 (tp40) REVERT: H 75 LYS cc_start: 0.9480 (tppt) cc_final: 0.9262 (tppt) REVERT: H 115 GLN cc_start: 0.8561 (mp10) cc_final: 0.8347 (mp10) REVERT: L 4 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7311 (pt) REVERT: L 42 LYS cc_start: 0.8370 (mppt) cc_final: 0.7961 (mptt) REVERT: L 45 ARG cc_start: 0.7478 (mtm110) cc_final: 0.7208 (ttp-110) REVERT: L 70 GLU cc_start: 0.7978 (pp20) cc_final: 0.7184 (pp20) REVERT: L 85 ASP cc_start: 0.7837 (m-30) cc_final: 0.7568 (m-30) REVERT: L 103 ARG cc_start: 0.8579 (mmm160) cc_final: 0.8336 (mmm160) outliers start: 24 outliers final: 18 residues processed: 106 average time/residue: 0.0764 time to fit residues: 10.1956 Evaluate side-chains 113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.111159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.086539 restraints weight = 10881.815| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 5.03 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4487 Z= 0.203 Angle : 0.779 9.971 6113 Z= 0.382 Chirality : 0.049 0.354 687 Planarity : 0.005 0.049 766 Dihedral : 7.195 56.165 792 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.33 % Favored : 89.48 % Rotamer: Outliers : 4.54 % Allowed : 18.14 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.36), residues: 523 helix: 1.61 (1.90), residues: 11 sheet: -0.60 (0.45), residues: 147 loop : -1.98 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 38 TYR 0.018 0.002 TYR H 50 PHE 0.010 0.002 PHE A 238 TRP 0.016 0.002 TRP A 258 HIS 0.005 0.002 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 4472) covalent geometry : angle 0.72158 ( 6073) SS BOND : bond 0.00211 ( 5) SS BOND : angle 1.16116 ( 10) hydrogen bonds : bond 0.02993 ( 89) hydrogen bonds : angle 6.26982 ( 231) link_BETA1-4 : bond 0.00418 ( 3) link_BETA1-4 : angle 1.24557 ( 9) link_NAG-ASN : bond 0.00973 ( 7) link_NAG-ASN : angle 4.96554 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 115 GLN cc_start: 0.8921 (mm110) cc_final: 0.8660 (mm-40) REVERT: A 173 GLN cc_start: 0.8564 (tp40) cc_final: 0.8148 (tp40) REVERT: A 190 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7548 (mtt-85) REVERT: A 314 GLN cc_start: 0.7175 (tp40) cc_final: 0.6929 (tp40) REVERT: H 57 ARG cc_start: 0.8274 (mmt-90) cc_final: 0.7966 (mmt-90) REVERT: H 72 ASP cc_start: 0.8043 (p0) cc_final: 0.7592 (p0) REVERT: H 82 MET cc_start: 0.7410 (tpt) cc_final: 0.7102 (tpt) REVERT: H 100 TYR cc_start: 0.9358 (m-80) cc_final: 0.9105 (m-80) REVERT: H 115 GLN cc_start: 0.8578 (mp10) cc_final: 0.8320 (mp10) REVERT: L 4 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7329 (pt) REVERT: L 45 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7354 (ttp-110) REVERT: L 70 GLU cc_start: 0.8176 (pp20) cc_final: 0.7500 (pp20) REVERT: L 85 ASP cc_start: 0.7807 (m-30) cc_final: 0.7511 (m-30) REVERT: L 103 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8148 (mmm160) outliers start: 21 outliers final: 17 residues processed: 110 average time/residue: 0.0694 time to fit residues: 9.6332 Evaluate side-chains 115 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.112153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.087456 restraints weight = 10814.300| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 5.10 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4487 Z= 0.151 Angle : 0.784 10.484 6113 Z= 0.379 Chirality : 0.049 0.340 687 Planarity : 0.005 0.049 766 Dihedral : 7.141 56.368 792 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.99 % Favored : 90.82 % Rotamer: Outliers : 3.46 % Allowed : 20.30 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.36), residues: 523 helix: 1.57 (1.89), residues: 11 sheet: -0.57 (0.45), residues: 147 loop : -1.92 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.018 0.002 TYR H 50 PHE 0.016 0.002 PHE A 157 TRP 0.009 0.001 TRP H 36 HIS 0.006 0.001 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4472) covalent geometry : angle 0.73000 ( 6073) SS BOND : bond 0.00211 ( 5) SS BOND : angle 0.89488 ( 10) hydrogen bonds : bond 0.02854 ( 89) hydrogen bonds : angle 6.13347 ( 231) link_BETA1-4 : bond 0.00559 ( 3) link_BETA1-4 : angle 1.21532 ( 9) link_NAG-ASN : bond 0.00979 ( 7) link_NAG-ASN : angle 4.88898 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8198 (tm-30) REVERT: A 115 GLN cc_start: 0.8942 (mm110) cc_final: 0.8688 (mm-40) REVERT: A 132 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 173 GLN cc_start: 0.8579 (tp40) cc_final: 0.8159 (tp40) REVERT: A 190 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7522 (mtt-85) REVERT: A 314 GLN cc_start: 0.7097 (tp40) cc_final: 0.6852 (tp40) REVERT: H 57 ARG cc_start: 0.8307 (mmt-90) cc_final: 0.7963 (mmt-90) REVERT: H 72 ASP cc_start: 0.7973 (p0) cc_final: 0.7545 (p0) REVERT: H 76 ASN cc_start: 0.7734 (t0) cc_final: 0.7512 (t0) REVERT: H 100 TYR cc_start: 0.9301 (m-80) cc_final: 0.9059 (m-80) REVERT: H 115 GLN cc_start: 0.8561 (mp10) cc_final: 0.8293 (mp10) REVERT: L 4 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7199 (pt) REVERT: L 45 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7337 (ttp-110) REVERT: L 70 GLU cc_start: 0.8196 (pp20) cc_final: 0.7577 (pp20) REVERT: L 85 ASP cc_start: 0.7736 (m-30) cc_final: 0.7429 (m-30) outliers start: 16 outliers final: 14 residues processed: 103 average time/residue: 0.0657 time to fit residues: 8.5938 Evaluate side-chains 113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 0.0050 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.113593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.089317 restraints weight = 10822.235| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 5.05 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4487 Z= 0.138 Angle : 0.776 10.256 6113 Z= 0.374 Chirality : 0.049 0.347 687 Planarity : 0.005 0.052 766 Dihedral : 7.005 56.304 792 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 3.24 % Allowed : 20.30 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.36), residues: 523 helix: 1.53 (1.90), residues: 11 sheet: -0.67 (0.44), residues: 150 loop : -1.87 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.016 0.002 TYR H 50 PHE 0.010 0.001 PHE A 318 TRP 0.011 0.001 TRP H 36 HIS 0.005 0.001 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4472) covalent geometry : angle 0.72350 ( 6073) SS BOND : bond 0.00192 ( 5) SS BOND : angle 0.75024 ( 10) hydrogen bonds : bond 0.02675 ( 89) hydrogen bonds : angle 6.01065 ( 231) link_BETA1-4 : bond 0.00548 ( 3) link_BETA1-4 : angle 1.12125 ( 9) link_NAG-ASN : bond 0.00947 ( 7) link_NAG-ASN : angle 4.79320 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 115 GLN cc_start: 0.8969 (mm110) cc_final: 0.8725 (mm-40) REVERT: A 173 GLN cc_start: 0.8543 (tp40) cc_final: 0.8166 (tp40) REVERT: A 190 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7543 (mtt-85) REVERT: A 298 GLU cc_start: 0.7299 (pt0) cc_final: 0.6596 (pt0) REVERT: A 314 GLN cc_start: 0.7034 (tp40) cc_final: 0.6795 (tp40) REVERT: H 57 ARG cc_start: 0.8298 (mmt-90) cc_final: 0.7938 (mmt-90) REVERT: H 67 PHE cc_start: 0.7731 (m-80) cc_final: 0.7414 (m-80) REVERT: H 72 ASP cc_start: 0.7824 (p0) cc_final: 0.7491 (p0) REVERT: H 115 GLN cc_start: 0.8569 (mp10) cc_final: 0.8290 (mp10) REVERT: L 4 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7075 (pt) REVERT: L 45 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7287 (ttp-110) REVERT: L 70 GLU cc_start: 0.8213 (pp20) cc_final: 0.7732 (pp20) REVERT: L 72 PHE cc_start: 0.7816 (m-80) cc_final: 0.7199 (m-80) REVERT: L 85 ASP cc_start: 0.7757 (m-30) cc_final: 0.7300 (m-30) outliers start: 15 outliers final: 12 residues processed: 108 average time/residue: 0.0675 time to fit residues: 9.3014 Evaluate side-chains 111 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 30 optimal weight: 0.0270 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.113121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088894 restraints weight = 10746.352| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 5.01 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4487 Z= 0.154 Angle : 0.789 10.301 6113 Z= 0.390 Chirality : 0.049 0.347 687 Planarity : 0.005 0.050 766 Dihedral : 6.996 56.183 792 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 3.67 % Allowed : 20.73 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.36), residues: 523 helix: 1.52 (1.88), residues: 11 sheet: -0.66 (0.43), residues: 150 loop : -1.78 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 38 TYR 0.017 0.002 TYR H 58 PHE 0.010 0.001 PHE A 157 TRP 0.016 0.001 TRP H 36 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4472) covalent geometry : angle 0.73905 ( 6073) SS BOND : bond 0.00155 ( 5) SS BOND : angle 0.72670 ( 10) hydrogen bonds : bond 0.02752 ( 89) hydrogen bonds : angle 5.92673 ( 231) link_BETA1-4 : bond 0.00511 ( 3) link_BETA1-4 : angle 1.12293 ( 9) link_NAG-ASN : bond 0.00912 ( 7) link_NAG-ASN : angle 4.74803 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8205 (tm-30) REVERT: A 115 GLN cc_start: 0.8974 (mm110) cc_final: 0.8731 (mm-40) REVERT: A 173 GLN cc_start: 0.8552 (tp40) cc_final: 0.8177 (tp40) REVERT: A 190 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7498 (mtt-85) REVERT: A 314 GLN cc_start: 0.7007 (tp40) cc_final: 0.6771 (tp40) REVERT: H 57 ARG cc_start: 0.8422 (mmt-90) cc_final: 0.7888 (mmt-90) REVERT: H 67 PHE cc_start: 0.7625 (m-80) cc_final: 0.7285 (m-80) REVERT: H 72 ASP cc_start: 0.7800 (p0) cc_final: 0.7428 (p0) REVERT: H 100 TYR cc_start: 0.9271 (m-10) cc_final: 0.9051 (m-10) REVERT: H 115 GLN cc_start: 0.8554 (mp10) cc_final: 0.8270 (mp10) REVERT: L 4 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7057 (pt) REVERT: L 45 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7386 (ttp-110) REVERT: L 70 GLU cc_start: 0.8181 (pp20) cc_final: 0.7648 (pp20) REVERT: L 85 ASP cc_start: 0.7728 (m-30) cc_final: 0.7397 (m-30) outliers start: 17 outliers final: 14 residues processed: 104 average time/residue: 0.0657 time to fit residues: 8.7008 Evaluate side-chains 111 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.113385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.088914 restraints weight = 10763.795| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 5.08 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.172 4487 Z= 0.308 Angle : 1.291 59.191 6113 Z= 0.767 Chirality : 0.051 0.355 687 Planarity : 0.006 0.068 766 Dihedral : 7.116 56.188 792 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.56 % Favored : 90.25 % Rotamer: Outliers : 3.67 % Allowed : 21.38 % Favored : 74.95 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.98 (0.36), residues: 523 helix: 1.52 (1.88), residues: 11 sheet: -0.72 (0.44), residues: 150 loop : -1.77 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.082 0.004 TYR H 58 PHE 0.011 0.001 PHE A 157 TRP 0.013 0.001 TRP H 36 HIS 0.003 0.001 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00608 ( 4472) covalent geometry : angle 1.26355 ( 6073) SS BOND : bond 0.00150 ( 5) SS BOND : angle 0.69578 ( 10) hydrogen bonds : bond 0.02740 ( 89) hydrogen bonds : angle 5.92574 ( 231) link_BETA1-4 : bond 0.00654 ( 3) link_BETA1-4 : angle 1.20293 ( 9) link_NAG-ASN : bond 0.00910 ( 7) link_NAG-ASN : angle 4.74994 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1067.46 seconds wall clock time: 18 minutes 59.48 seconds (1139.48 seconds total)