Starting phenix.real_space_refine on Wed Jul 23 22:20:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uaq_26430/07_2025/7uaq_26430.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uaq_26430/07_2025/7uaq_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_26430/07_2025/7uaq_26430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uaq_26430/07_2025/7uaq_26430.map" model { file = "/net/cci-nas-00/data/ceres_data/7uaq_26430/07_2025/7uaq_26430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uaq_26430/07_2025/7uaq_26430.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.17, per 1000 atoms: 0.96 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: 1.05 Conformation dependent library (CDL) restraints added in 558.8 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: 0.73 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: 0.99 Time building geometry restraints manager: 1.27 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.740 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:4.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.002 TRP A 152 HIS 0.008 0.002 HIS H 106 PHE 0.032 0.003 PHE L 72 TYR 0.032 0.002 TYR A 144 ARG 0.007 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.01575 ( 7) link_NAG-ASN : angle 8.64520 ( 21) link_BETA1-4 : bond 0.00514 ( 3) link_BETA1-4 : angle 1.66685 ( 9) hydrogen bonds : bond 0.28573 ( 89) hydrogen bonds : angle 10.97881 ( 231) SS BOND : bond 0.00625 ( 5) SS BOND : angle 3.78987 ( 10) covalent geometry : bond 0.00611 ( 4472) covalent geometry : angle 1.18662 ( 6073) *********************** 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 : 0.396 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: 0.2594 time to fit residues: 44.7344 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 : 0.583 ------------------------------------------------------------------------------- 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 43 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 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 = 0.4007 r_free = 0.4007 target = 0.117308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.093377 restraints weight = 10798.189| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 4.96 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4487 Z= 0.219 Angle : 0.945 11.787 6113 Z= 0.463 Chirality : 0.054 0.353 687 Planarity : 0.006 0.068 766 Dihedral : 8.559 57.263 794 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.38 % Allowed : 13.61 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.34), residues: 523 helix: 0.84 (1.68), residues: 11 sheet: -0.73 (0.43), residues: 145 loop : -2.24 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 35 HIS 0.006 0.002 HIS H 98 PHE 0.024 0.002 PHE A 238 TYR 0.023 0.002 TYR H 50 ARG 0.007 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.01376 ( 7) link_NAG-ASN : angle 5.94914 ( 21) link_BETA1-4 : bond 0.00700 ( 3) link_BETA1-4 : angle 1.41093 ( 9) hydrogen bonds : bond 0.04427 ( 89) hydrogen bonds : angle 7.10414 ( 231) SS BOND : bond 0.00777 ( 5) SS BOND : angle 2.54539 ( 10) covalent geometry : bond 0.00479 ( 4472) covalent geometry : angle 0.87307 ( 6073) *********************** 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 108 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 190 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7622 (mtt-85) REVERT: A 211 ASN cc_start: 0.8688 (p0) cc_final: 0.8444 (p0) REVERT: A 298 GLU cc_start: 0.7162 (pt0) cc_final: 0.6325 (pt0) REVERT: A 314 GLN cc_start: 0.6829 (tp40) cc_final: 0.6322 (tp40) REVERT: L 4 LEU cc_start: 0.7522 (pt) cc_final: 0.7151 (pt) REVERT: L 85 ASP cc_start: 0.7573 (m-30) cc_final: 0.6927 (m-30) outliers start: 11 outliers final: 7 residues processed: 105 average time/residue: 0.1730 time to fit residues: 22.7998 Evaluate side-chains 99 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 ASN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** ** L 89 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 = 0.3970 r_free = 0.3970 target = 0.115187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.090981 restraints weight = 10926.622| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 5.03 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4487 Z= 0.191 Angle : 0.861 12.195 6113 Z= 0.419 Chirality : 0.052 0.325 687 Planarity : 0.005 0.050 766 Dihedral : 7.990 56.994 792 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 3.46 % Allowed : 14.47 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.35), residues: 523 helix: 1.29 (1.83), residues: 11 sheet: -0.47 (0.43), residues: 147 loop : -2.14 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.005 0.001 HIS A 66 PHE 0.013 0.002 PHE A 220 TYR 0.021 0.002 TYR H 50 ARG 0.005 0.001 ARG L 103 Details of bonding type rmsd link_NAG-ASN : bond 0.01089 ( 7) link_NAG-ASN : angle 5.57013 ( 21) link_BETA1-4 : bond 0.00545 ( 3) link_BETA1-4 : angle 1.33163 ( 9) hydrogen bonds : bond 0.03482 ( 89) hydrogen bonds : angle 6.40016 ( 231) SS BOND : bond 0.00374 ( 5) SS BOND : angle 1.93855 ( 10) covalent geometry : bond 0.00432 ( 4472) covalent geometry : angle 0.79400 ( 6073) *********************** 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: 16 poor density : 95 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 132 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 153 MET cc_start: 0.7541 (ptt) cc_final: 0.7202 (ptt) REVERT: A 169 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7954 (tm-30) REVERT: A 190 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7701 (mtt-85) REVERT: A 314 GLN cc_start: 0.6908 (tp40) cc_final: 0.6631 (tp40) REVERT: H 105 TYR cc_start: 0.6465 (m-10) cc_final: 0.6253 (m-10) REVERT: H 107 SER cc_start: 0.7257 (p) cc_final: 0.6809 (p) REVERT: L 4 LEU cc_start: 0.7566 (pt) cc_final: 0.7234 (pt) REVERT: L 39 GLN cc_start: 0.8106 (tp-100) cc_final: 0.7585 (tm-30) REVERT: L 42 LYS cc_start: 0.8533 (mppt) cc_final: 0.7892 (mmtm) REVERT: L 70 GLU cc_start: 0.7782 (pp20) cc_final: 0.6896 (pp20) outliers start: 16 outliers final: 13 residues processed: 105 average time/residue: 0.1765 time to fit residues: 22.9653 Evaluate side-chains 104 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 25 LEU 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 34 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3968 r_free = 0.3968 target = 0.115237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.091272 restraints weight = 10947.824| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 5.04 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4487 Z= 0.150 Angle : 0.797 11.350 6113 Z= 0.383 Chirality : 0.050 0.326 687 Planarity : 0.005 0.049 766 Dihedral : 7.456 56.936 792 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.56 % Favored : 90.25 % Rotamer: Outliers : 4.10 % Allowed : 14.69 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.35), residues: 523 helix: 1.35 (1.85), residues: 11 sheet: -0.44 (0.44), residues: 147 loop : -2.06 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.006 0.002 HIS H 98 PHE 0.009 0.002 PHE A 318 TYR 0.022 0.002 TYR H 50 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.01107 ( 7) link_NAG-ASN : angle 5.31194 ( 21) link_BETA1-4 : bond 0.00539 ( 3) link_BETA1-4 : angle 1.26009 ( 9) hydrogen bonds : bond 0.03120 ( 89) hydrogen bonds : angle 6.12502 ( 231) SS BOND : bond 0.00350 ( 5) SS BOND : angle 1.66343 ( 10) covalent geometry : bond 0.00342 ( 4472) covalent geometry : angle 0.73173 ( 6073) *********************** 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 119 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8226 (tm-30) REVERT: A 132 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7543 (tm-30) REVERT: A 169 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7982 (tm-30) REVERT: A 190 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7598 (mtt-85) REVERT: A 298 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6056 (pt0) REVERT: A 314 GLN cc_start: 0.6878 (tp40) cc_final: 0.6600 (tp40) REVERT: H 29 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8307 (t80) REVERT: H 57 ARG cc_start: 0.8356 (mmt-90) cc_final: 0.7877 (mmt-90) REVERT: H 72 ASP cc_start: 0.7214 (p0) cc_final: 0.6983 (p0) REVERT: H 100 TYR cc_start: 0.9265 (m-80) cc_final: 0.9045 (m-80) REVERT: L 4 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7208 (pt) REVERT: L 39 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7635 (tm-30) REVERT: L 45 ARG cc_start: 0.7406 (mtm110) cc_final: 0.7074 (ttp-110) REVERT: L 70 GLU cc_start: 0.7994 (pp20) cc_final: 0.7355 (pp20) outliers start: 19 outliers final: 10 residues processed: 111 average time/residue: 0.1913 time to fit residues: 26.6080 Evaluate side-chains 109 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 271 GLN 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 62 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 50 LEU Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.114009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.089917 restraints weight = 11040.078| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 5.11 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4487 Z= 0.160 Angle : 0.776 11.129 6113 Z= 0.375 Chirality : 0.049 0.335 687 Planarity : 0.005 0.047 766 Dihedral : 7.245 56.583 792 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 4.54 % Allowed : 15.98 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.36), residues: 523 helix: 1.46 (1.86), residues: 11 sheet: -0.46 (0.44), residues: 147 loop : -1.96 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 258 HIS 0.005 0.001 HIS H 98 PHE 0.009 0.001 PHE A 318 TYR 0.020 0.002 TYR H 108 ARG 0.006 0.001 ARG L 103 Details of bonding type rmsd link_NAG-ASN : bond 0.01063 ( 7) link_NAG-ASN : angle 5.23428 ( 21) link_BETA1-4 : bond 0.00460 ( 3) link_BETA1-4 : angle 1.21088 ( 9) hydrogen bonds : bond 0.03032 ( 89) hydrogen bonds : angle 6.08662 ( 231) SS BOND : bond 0.00336 ( 5) SS BOND : angle 1.46753 ( 10) covalent geometry : bond 0.00363 ( 4472) covalent geometry : angle 0.71145 ( 6073) *********************** 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 117 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 69 HIS cc_start: 0.8111 (t-90) cc_final: 0.7831 (t-90) REVERT: A 115 GLN cc_start: 0.8778 (mm110) cc_final: 0.8521 (mm-40) REVERT: A 132 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 169 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8024 (tm-30) REVERT: A 190 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7669 (mtp85) REVERT: A 211 ASN cc_start: 0.8566 (p0) cc_final: 0.8355 (p0) REVERT: A 314 GLN cc_start: 0.7105 (tp40) cc_final: 0.6785 (tp40) REVERT: H 57 ARG cc_start: 0.8395 (mmt-90) cc_final: 0.7898 (mmt-90) REVERT: L 4 LEU cc_start: 0.7619 (pt) cc_final: 0.7300 (pt) REVERT: L 39 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7656 (tm-30) REVERT: L 45 ARG cc_start: 0.7462 (mtm110) cc_final: 0.7115 (ttp-110) REVERT: L 70 GLU cc_start: 0.7901 (pp20) cc_final: 0.7265 (pp20) REVERT: L 103 ARG cc_start: 0.8501 (mmm160) cc_final: 0.8095 (mmm160) outliers start: 21 outliers final: 16 residues processed: 108 average time/residue: 0.1664 time to fit residues: 22.6970 Evaluate side-chains 110 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 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 50 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3926 r_free = 0.3926 target = 0.112505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.088367 restraints weight = 10868.763| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 5.01 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 0.041 4487 Z= 0.178 Angle : 0.770 10.288 6113 Z= 0.373 Chirality : 0.049 0.307 687 Planarity : 0.005 0.047 766 Dihedral : 7.245 56.229 792 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.33 % Favored : 89.48 % Rotamer: Outliers : 4.75 % Allowed : 15.98 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.36), residues: 523 helix: 1.71 (2.00), residues: 11 sheet: -0.56 (0.44), residues: 147 loop : -1.87 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 258 HIS 0.005 0.001 HIS H 98 PHE 0.010 0.001 PHE A 318 TYR 0.018 0.002 TYR H 50 ARG 0.004 0.001 ARG L 103 Details of bonding type rmsd link_NAG-ASN : bond 0.01029 ( 7) link_NAG-ASN : angle 5.10105 ( 21) link_BETA1-4 : bond 0.00432 ( 3) link_BETA1-4 : angle 1.23572 ( 9) hydrogen bonds : bond 0.02852 ( 89) hydrogen bonds : angle 6.05527 ( 231) SS BOND : bond 0.00459 ( 5) SS BOND : angle 1.67048 ( 10) covalent geometry : bond 0.00408 ( 4472) covalent geometry : angle 0.70693 ( 6073) *********************** 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: 22 poor density : 98 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 115 GLN cc_start: 0.8825 (mm110) cc_final: 0.8567 (mm-40) REVERT: A 132 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 169 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8047 (tm-30) REVERT: A 173 GLN cc_start: 0.8608 (tp40) cc_final: 0.8192 (tp40) REVERT: A 190 ARG cc_start: 0.7999 (mtt-85) cc_final: 0.7584 (mtt-85) REVERT: A 211 ASN cc_start: 0.8556 (p0) cc_final: 0.8326 (p0) REVERT: A 314 GLN cc_start: 0.7074 (tp40) cc_final: 0.6818 (tp40) REVERT: H 57 ARG cc_start: 0.8421 (mmt-90) cc_final: 0.7918 (mmt-90) REVERT: H 82 MET cc_start: 0.7476 (tpt) cc_final: 0.7057 (tpt) REVERT: L 4 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7310 (pt) REVERT: L 39 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7708 (tm-30) REVERT: L 45 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7291 (ttp-110) REVERT: L 70 GLU cc_start: 0.8050 (pp20) cc_final: 0.7303 (pp20) outliers start: 22 outliers final: 18 residues processed: 108 average time/residue: 0.1601 time to fit residues: 21.7691 Evaluate side-chains 108 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 188 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.113141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.088516 restraints weight = 10908.009| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 5.10 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4487 Z= 0.152 Angle : 0.767 10.429 6113 Z= 0.372 Chirality : 0.049 0.348 687 Planarity : 0.004 0.047 766 Dihedral : 7.127 56.422 792 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.54 % Allowed : 17.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.36), residues: 523 helix: 1.49 (1.90), residues: 11 sheet: -0.50 (0.44), residues: 149 loop : -1.85 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.005 0.001 HIS H 98 PHE 0.014 0.001 PHE H 67 TYR 0.018 0.002 TYR H 50 ARG 0.005 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.01027 ( 7) link_NAG-ASN : angle 5.00474 ( 21) link_BETA1-4 : bond 0.00472 ( 3) link_BETA1-4 : angle 1.17058 ( 9) hydrogen bonds : bond 0.02725 ( 89) hydrogen bonds : angle 6.09448 ( 231) SS BOND : bond 0.00345 ( 5) SS BOND : angle 1.98159 ( 10) covalent geometry : bond 0.00347 ( 4472) covalent geometry : angle 0.70517 ( 6073) *********************** 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 114 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 115 GLN cc_start: 0.8887 (mm110) cc_final: 0.8621 (mm-40) REVERT: A 132 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 169 GLU cc_start: 0.8264 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 173 GLN cc_start: 0.8596 (tp40) cc_final: 0.8244 (tp40) REVERT: A 190 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7530 (mtt-85) REVERT: A 211 ASN cc_start: 0.8605 (p0) cc_final: 0.8351 (p0) REVERT: A 298 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6463 (pt0) REVERT: A 314 GLN cc_start: 0.7081 (tp40) cc_final: 0.6817 (tp40) REVERT: H 57 ARG cc_start: 0.8418 (mmt-90) cc_final: 0.7942 (mmt-90) REVERT: L 4 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7258 (pt) REVERT: L 39 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7693 (tm-30) REVERT: L 45 ARG cc_start: 0.7576 (mtm110) cc_final: 0.7314 (ttp-110) REVERT: L 70 GLU cc_start: 0.8165 (pp20) cc_final: 0.7577 (pp20) outliers start: 21 outliers final: 17 residues processed: 103 average time/residue: 0.1620 time to fit residues: 21.2600 Evaluate side-chains 109 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 159 VAL 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 50 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.112963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.088632 restraints weight = 10852.287| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 5.06 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 0.029 4487 Z= 0.149 Angle : 0.771 10.271 6113 Z= 0.370 Chirality : 0.048 0.338 687 Planarity : 0.004 0.048 766 Dihedral : 7.087 56.202 792 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.75 % Favored : 90.06 % Rotamer: Outliers : 4.10 % Allowed : 19.01 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.36), residues: 523 helix: 1.42 (1.87), residues: 11 sheet: -0.46 (0.44), residues: 149 loop : -1.74 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.004 0.001 HIS A 69 PHE 0.010 0.001 PHE A 318 TYR 0.018 0.002 TYR H 97 ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00966 ( 7) link_NAG-ASN : angle 4.94647 ( 21) link_BETA1-4 : bond 0.00519 ( 3) link_BETA1-4 : angle 1.16674 ( 9) hydrogen bonds : bond 0.02705 ( 89) hydrogen bonds : angle 5.99316 ( 231) SS BOND : bond 0.00165 ( 5) SS BOND : angle 1.14075 ( 10) covalent geometry : bond 0.00338 ( 4472) covalent geometry : angle 0.71390 ( 6073) *********************** 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 115 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 115 GLN cc_start: 0.8895 (mm110) cc_final: 0.8639 (mm-40) REVERT: A 132 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 169 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 173 GLN cc_start: 0.8616 (tp40) cc_final: 0.8275 (tp40) REVERT: A 190 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7559 (mtt-85) REVERT: A 211 ASN cc_start: 0.8641 (p0) cc_final: 0.8367 (p0) REVERT: A 314 GLN cc_start: 0.7049 (tp40) cc_final: 0.6810 (tp40) REVERT: H 57 ARG cc_start: 0.8426 (mmt-90) cc_final: 0.7965 (mmt-90) REVERT: H 76 ASN cc_start: 0.7604 (t0) cc_final: 0.7397 (t0) REVERT: L 4 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7192 (pt) REVERT: L 39 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7726 (tm-30) REVERT: L 45 ARG cc_start: 0.7656 (mtm110) cc_final: 0.7399 (ttp-110) REVERT: L 70 GLU cc_start: 0.8109 (pp20) cc_final: 0.7519 (pp20) outliers start: 19 outliers final: 15 residues processed: 104 average time/residue: 0.1578 time to fit residues: 20.9122 Evaluate side-chains 109 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 30 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.112442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.088003 restraints weight = 10863.843| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 5.05 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4487 Z= 0.154 Angle : 0.771 9.991 6113 Z= 0.370 Chirality : 0.048 0.344 687 Planarity : 0.004 0.047 766 Dihedral : 7.046 56.212 792 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.37), residues: 523 helix: 1.37 (1.88), residues: 11 sheet: -0.54 (0.43), residues: 155 loop : -1.67 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.005 0.001 HIS H 106 PHE 0.011 0.001 PHE H 67 TYR 0.016 0.002 TYR H 50 ARG 0.005 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00954 ( 7) link_NAG-ASN : angle 4.84527 ( 21) link_BETA1-4 : bond 0.00516 ( 3) link_BETA1-4 : angle 1.15650 ( 9) hydrogen bonds : bond 0.02634 ( 89) hydrogen bonds : angle 6.02561 ( 231) SS BOND : bond 0.00192 ( 5) SS BOND : angle 0.99176 ( 10) covalent geometry : bond 0.00354 ( 4472) covalent geometry : angle 0.71622 ( 6073) *********************** 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 110 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8324 (tm-30) REVERT: A 115 GLN cc_start: 0.8934 (mm110) cc_final: 0.8681 (mm-40) REVERT: A 169 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8062 (tm-30) REVERT: A 173 GLN cc_start: 0.8620 (tp40) cc_final: 0.8278 (tp40) REVERT: A 190 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7534 (mtt-85) REVERT: A 211 ASN cc_start: 0.8675 (p0) cc_final: 0.8418 (p0) REVERT: A 314 GLN cc_start: 0.7079 (tp40) cc_final: 0.6839 (tp40) REVERT: H 57 ARG cc_start: 0.8451 (mmt-90) cc_final: 0.8001 (mmt-90) REVERT: H 72 ASP cc_start: 0.8159 (p0) cc_final: 0.7656 (p0) REVERT: H 76 ASN cc_start: 0.7753 (t0) cc_final: 0.7482 (t0) REVERT: L 4 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7116 (pt) REVERT: L 39 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7715 (tm-30) REVERT: L 45 ARG cc_start: 0.7667 (mtm110) cc_final: 0.7395 (ttp-110) REVERT: L 70 GLU cc_start: 0.8141 (pp20) cc_final: 0.7585 (pp20) outliers start: 16 outliers final: 14 residues processed: 101 average time/residue: 0.1622 time to fit residues: 20.7095 Evaluate side-chains 105 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 5 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 207 HIS ** 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 = 0.3947 r_free = 0.3947 target = 0.113423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.089305 restraints weight = 10708.338| |-----------------------------------------------------------------------------| 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: 0.7729 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4487 Z= 0.138 Angle : 0.771 10.080 6113 Z= 0.370 Chirality : 0.048 0.340 687 Planarity : 0.004 0.046 766 Dihedral : 6.971 56.319 792 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 3.02 % Allowed : 21.81 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.37), residues: 523 helix: 1.27 (1.88), residues: 11 sheet: -0.55 (0.43), residues: 150 loop : -1.60 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS H 98 PHE 0.010 0.001 PHE A 318 TYR 0.016 0.001 TYR H 50 ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00945 ( 7) link_NAG-ASN : angle 4.74668 ( 21) link_BETA1-4 : bond 0.00533 ( 3) link_BETA1-4 : angle 1.09102 ( 9) hydrogen bonds : bond 0.02549 ( 89) hydrogen bonds : angle 5.95048 ( 231) SS BOND : bond 0.00202 ( 5) SS BOND : angle 0.85408 ( 10) covalent geometry : bond 0.00315 ( 4472) covalent geometry : angle 0.71912 ( 6073) ********************** 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 106 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8334 (tm-30) REVERT: A 115 GLN cc_start: 0.8957 (mm110) cc_final: 0.8711 (mm-40) REVERT: A 169 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8012 (tm-30) REVERT: A 173 GLN cc_start: 0.8597 (tp40) cc_final: 0.8262 (tp40) REVERT: A 190 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7525 (mtt-85) REVERT: A 211 ASN cc_start: 0.8663 (p0) cc_final: 0.8432 (p0) REVERT: A 314 GLN cc_start: 0.6993 (tp40) cc_final: 0.6761 (tp40) REVERT: H 57 ARG cc_start: 0.8466 (mmt-90) cc_final: 0.8041 (mmt-90) REVERT: H 72 ASP cc_start: 0.8051 (p0) cc_final: 0.7597 (p0) REVERT: H 76 ASN cc_start: 0.7577 (t0) cc_final: 0.7373 (t0) REVERT: H 99 TYR cc_start: 0.9011 (t80) cc_final: 0.8743 (t80) REVERT: L 4 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7044 (pt) REVERT: L 39 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7712 (tm-30) REVERT: L 45 ARG cc_start: 0.7660 (mtm110) cc_final: 0.7401 (ttp-110) REVERT: L 70 GLU cc_start: 0.8129 (pp20) cc_final: 0.7522 (pp20) outliers start: 14 outliers final: 12 residues processed: 100 average time/residue: 0.1617 time to fit residues: 20.5893 Evaluate side-chains 103 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain L residue 25 LEU 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 48 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 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 = 0.3933 r_free = 0.3933 target = 0.112452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.088138 restraints weight = 10795.548| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 5.05 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4887 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= 0.157 Angle : 0.769 9.627 6113 Z= 0.370 Chirality : 0.048 0.345 687 Planarity : 0.004 0.046 766 Dihedral : 6.962 56.093 792 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 2.81 % Allowed : 21.38 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.37), residues: 523 helix: 1.30 (1.87), residues: 11 sheet: -0.58 (0.43), residues: 150 loop : -1.56 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.005 0.001 HIS H 106 PHE 0.011 0.001 PHE H 67 TYR 0.016 0.002 TYR H 108 ARG 0.005 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00942 ( 7) link_NAG-ASN : angle 4.68805 ( 21) link_BETA1-4 : bond 0.00536 ( 3) link_BETA1-4 : angle 1.14526 ( 9) hydrogen bonds : bond 0.02602 ( 89) hydrogen bonds : angle 5.97336 ( 231) SS BOND : bond 0.00217 ( 5) SS BOND : angle 0.89072 ( 10) covalent geometry : bond 0.00361 ( 4472) covalent geometry : angle 0.71877 ( 6073) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2864.58 seconds wall clock time: 50 minutes 57.57 seconds (3057.57 seconds total)