Starting phenix.real_space_refine on Tue Jul 29 08:03:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tio_41297/07_2025/8tio_41297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tio_41297/07_2025/8tio_41297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tio_41297/07_2025/8tio_41297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tio_41297/07_2025/8tio_41297.map" model { file = "/net/cci-nas-00/data/ceres_data/8tio_41297/07_2025/8tio_41297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tio_41297/07_2025/8tio_41297.cif" } resolution = 3.6 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= -0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 21 5.16 5 C 3564 2.51 5 N 944 2.21 5 O 1060 1.98 5 H 5573 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11164 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4840 Classifications: {'peptide': 299} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 275} Chain breaks: 8 Chain: "H" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3087 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 194} Chain breaks: 3 Chain: "L" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3115 Classifications: {'peptide': 204} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "R" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 122 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 6.35, per 1000 atoms: 0.57 Number of scatterers: 11164 At special positions: 0 Unit cell: (64.294, 105.4, 122.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 2 15.00 O 1060 8.00 N 944 7.00 C 3564 6.00 H 5573 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 801.8 milliseconds 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 18 sheets defined 4.1% alpha, 45.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.667A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 223 Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117 removed outlier: 3.584A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 8 " --> pdb=" O TPO R 355 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 10 " --> pdb=" O GLY R 353 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 5.879A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 87 removed outlier: 5.632A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A 80 " --> pdb=" O CYS A 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 82 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 53 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.130A pdb=" N TYR A 208 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA8, first strand: chain 'H' and resid 14 through 15 removed outlier: 5.836A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 14 through 15 removed outlier: 4.068A pdb=" N TYR H 121 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 139 through 143 removed outlier: 5.159A pdb=" N GLY H 158 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL H 201 " --> pdb=" O GLY H 158 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU H 160 " --> pdb=" O SER H 199 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER H 199 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS H 162 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU H 197 " --> pdb=" O LYS H 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR H 164 " --> pdb=" O TYR H 195 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL H 200 " --> pdb=" O HIS H 183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 139 through 143 removed outlier: 5.159A pdb=" N GLY H 158 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL H 201 " --> pdb=" O GLY H 158 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU H 160 " --> pdb=" O SER H 199 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER H 199 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS H 162 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU H 197 " --> pdb=" O LYS H 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR H 164 " --> pdb=" O TYR H 195 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 170 through 173 removed outlier: 4.188A pdb=" N TYR H 213 " --> pdb=" O VAL H 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB5, first strand: chain 'L' and resid 11 through 14 removed outlier: 7.194A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 35 through 39 removed outlier: 3.895A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 49 through 50 Processing sheet with id=AB8, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.932A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 145 through 150 212 hydrogen bonds defined for protein. 543 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: 4.11 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5558 1.03 - 1.23: 47 1.23 - 1.43: 2346 1.43 - 1.62: 3309 1.62 - 1.82: 27 Bond restraints: 11287 Sorted by residual: bond pdb=" CG2 TPO R 352 " pdb="HG23 TPO R 352 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" CG2 TPO R 355 " pdb="HG23 TPO R 355 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" CB TPO R 355 " pdb=" HB TPO R 355 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CG2 TPO R 352 " pdb="HG22 TPO R 352 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CB TPO R 352 " pdb=" HB TPO R 352 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 ... (remaining 11282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.64: 20399 12.64 - 25.28: 0 25.28 - 37.92: 0 37.92 - 50.56: 0 50.56 - 63.20: 1 Bond angle restraints: 20400 Sorted by residual: angle pdb=" C LEU R 354 " pdb=" N TPO R 355 " pdb=" H TPO R 355 " ideal model delta sigma weight residual 124.30 61.10 63.20 3.00e+00 1.11e-01 4.44e+02 angle pdb=" CB TPO R 355 " pdb=" OG1 TPO R 355 " pdb=" P TPO R 355 " ideal model delta sigma weight residual 119.31 106.91 12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB TPO R 352 " pdb=" OG1 TPO R 352 " pdb=" P TPO R 352 " ideal model delta sigma weight residual 119.31 107.58 11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" OG1 TPO R 352 " pdb=" P TPO R 352 " pdb=" O1P TPO R 352 " ideal model delta sigma weight residual 100.43 109.83 -9.40 3.00e+00 1.11e-01 9.82e+00 angle pdb=" OG1 TPO R 355 " pdb=" P TPO R 355 " pdb=" O1P TPO R 355 " ideal model delta sigma weight residual 100.43 109.29 -8.86 3.00e+00 1.11e-01 8.73e+00 ... (remaining 20395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4922 17.34 - 34.69: 349 34.69 - 52.03: 86 52.03 - 69.37: 23 69.37 - 86.72: 4 Dihedral angle restraints: 5384 sinusoidal: 2915 harmonic: 2469 Sorted by residual: dihedral pdb=" CA PRO L 114 " pdb=" C PRO L 114 " pdb=" N SER L 115 " pdb=" CA SER L 115 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA TYR H 116 " pdb=" C TYR H 116 " pdb=" N GLY H 117 " pdb=" CA GLY H 117 " ideal model delta harmonic sigma weight residual -180.00 -160.41 -19.59 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ASP L 171 " pdb=" C ASP L 171 " pdb=" N SER L 172 " pdb=" CA SER L 172 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 555 0.034 - 0.068: 222 0.068 - 0.101: 57 0.101 - 0.135: 46 0.135 - 0.169: 3 Chirality restraints: 883 Sorted by residual: chirality pdb=" CA VAL H 40 " pdb=" N VAL H 40 " pdb=" C VAL H 40 " pdb=" CB VAL H 40 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA VAL H 161 " pdb=" N VAL H 161 " pdb=" C VAL H 161 " pdb=" CB VAL H 161 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA VAL A 345 " pdb=" N VAL A 345 " pdb=" C VAL A 345 " pdb=" CB VAL A 345 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 880 not shown) Planarity restraints: 1624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 354 " 0.081 2.00e-02 2.50e+03 2.42e-01 5.85e+02 pdb=" N TPO R 355 " -0.413 2.00e-02 2.50e+03 pdb=" CA TPO R 355 " 0.135 2.00e-02 2.50e+03 pdb=" H TPO R 355 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 165 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO H 166 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO H 166 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 166 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 167 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO H 168 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO H 168 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 168 " 0.016 5.00e-02 4.00e+02 ... (remaining 1621 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 428 2.15 - 2.76: 21969 2.76 - 3.37: 30395 3.37 - 3.99: 40962 3.99 - 4.60: 63372 Nonbonded interactions: 157126 Sorted by model distance: nonbonded pdb=" OE1 GLN L 125 " pdb=" H SER L 132 " model vdw 1.534 2.450 nonbonded pdb=" H ASP L 168 " pdb=" O THR L 173 " model vdw 1.538 2.450 nonbonded pdb=" OD1 ASN A 299 " pdb=" HE2 HIS A 353 " model vdw 1.539 2.450 nonbonded pdb=" OE1 GLN H 42 " pdb="HE22 GLN L 39 " model vdw 1.565 2.450 nonbonded pdb=" H ASP A 29 " pdb=" O VAL A 171 " model vdw 1.565 2.450 ... (remaining 157121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.330 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: 0.170 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.660 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 5718 Z= 0.217 Angle : 0.621 12.401 7760 Z= 0.302 Chirality : 0.045 0.169 883 Planarity : 0.004 0.034 968 Dihedral : 11.828 86.717 2082 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.79 % Allowed : 9.11 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.95 (0.32), residues: 677 helix: 0.87 (1.04), residues: 23 sheet: -0.88 (0.29), residues: 333 loop : -1.87 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 PHE 0.010 0.001 PHE L 140 TYR 0.009 0.001 TYR A 272 ARG 0.002 0.000 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.13001 ( 200) hydrogen bonds : angle 7.20601 ( 543) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.79930 ( 8) covalent geometry : bond 0.00452 ( 5714) covalent geometry : angle 0.62069 ( 7752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.3739 (m-80) cc_final: 0.3351 (m-10) REVERT: A 298 THR cc_start: 0.5814 (OUTLIER) cc_final: 0.5578 (p) REVERT: H 21 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7432 (tt) REVERT: H 98 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.4255 (m-80) outliers start: 30 outliers final: 20 residues processed: 140 average time/residue: 0.4980 time to fit residues: 88.0868 Evaluate side-chains 98 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 173 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.202803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.185741 restraints weight = 19613.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.189369 restraints weight = 11765.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.191576 restraints weight = 7929.054| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5718 Z= 0.178 Angle : 0.607 5.564 7760 Z= 0.313 Chirality : 0.046 0.180 883 Planarity : 0.005 0.035 968 Dihedral : 9.126 86.111 810 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.95 % Allowed : 13.90 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.89 (0.33), residues: 677 helix: 0.45 (1.02), residues: 24 sheet: -0.83 (0.29), residues: 339 loop : -1.82 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.005 0.001 HIS A 210 PHE 0.014 0.002 PHE L 140 TYR 0.012 0.001 TYR A 272 ARG 0.004 0.001 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 200) hydrogen bonds : angle 6.40305 ( 543) SS BOND : bond 0.00375 ( 4) SS BOND : angle 1.21972 ( 8) covalent geometry : bond 0.00390 ( 5714) covalent geometry : angle 0.60634 ( 7752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 THR cc_start: 0.6003 (OUTLIER) cc_final: 0.5751 (p) REVERT: H 21 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7510 (tt) REVERT: H 98 TYR cc_start: 0.6310 (OUTLIER) cc_final: 0.4287 (m-80) outliers start: 31 outliers final: 23 residues processed: 106 average time/residue: 0.4486 time to fit residues: 63.2723 Evaluate side-chains 99 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 175 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.0030 chunk 5 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.204012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.189532 restraints weight = 19578.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.192312 restraints weight = 12387.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.194091 restraints weight = 8769.785| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5718 Z= 0.132 Angle : 0.549 5.624 7760 Z= 0.282 Chirality : 0.045 0.168 883 Planarity : 0.004 0.035 968 Dihedral : 8.710 86.740 805 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.63 % Allowed : 14.54 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.85 (0.33), residues: 677 helix: 0.76 (1.03), residues: 26 sheet: -0.73 (0.30), residues: 333 loop : -1.90 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.014 0.001 PHE A 277 TYR 0.009 0.001 TYR A 272 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 200) hydrogen bonds : angle 6.01272 ( 543) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.91467 ( 8) covalent geometry : bond 0.00294 ( 5714) covalent geometry : angle 0.54865 ( 7752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 THR cc_start: 0.5829 (OUTLIER) cc_final: 0.5566 (p) REVERT: H 21 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7536 (tt) REVERT: H 22 ARG cc_start: 0.7526 (ttt-90) cc_final: 0.7319 (ttt180) REVERT: H 98 TYR cc_start: 0.6373 (OUTLIER) cc_final: 0.4440 (m-80) outliers start: 29 outliers final: 24 residues processed: 101 average time/residue: 0.5232 time to fit residues: 70.4018 Evaluate side-chains 95 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** L 190 HIS ** 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 = 0.4450 r_free = 0.4450 target = 0.205654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.191652 restraints weight = 19367.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.194468 restraints weight = 12182.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.196351 restraints weight = 8482.734| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5718 Z= 0.113 Angle : 0.527 5.544 7760 Z= 0.271 Chirality : 0.045 0.163 883 Planarity : 0.004 0.034 968 Dihedral : 8.472 87.104 802 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.63 % Allowed : 14.54 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.68 (0.33), residues: 677 helix: 0.97 (1.05), residues: 26 sheet: -0.65 (0.30), residues: 333 loop : -1.77 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.013 0.001 HIS L 190 PHE 0.010 0.001 PHE L 140 TYR 0.008 0.001 TYR A 272 ARG 0.003 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.02911 ( 200) hydrogen bonds : angle 5.74455 ( 543) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.69537 ( 8) covalent geometry : bond 0.00250 ( 5714) covalent geometry : angle 0.52717 ( 7752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.2199 (mtp) cc_final: 0.1974 (mtp) REVERT: H 21 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7488 (tt) REVERT: H 22 ARG cc_start: 0.7428 (ttt-90) cc_final: 0.7103 (ttt180) REVERT: H 98 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.4426 (m-80) outliers start: 29 outliers final: 23 residues processed: 94 average time/residue: 0.5166 time to fit residues: 64.2109 Evaluate side-chains 89 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN H 218 ASN ** L 190 HIS ** 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 = 0.4431 r_free = 0.4431 target = 0.203263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.186644 restraints weight = 19336.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.190211 restraints weight = 11513.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.192611 restraints weight = 7691.014| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5718 Z= 0.144 Angle : 0.544 5.219 7760 Z= 0.281 Chirality : 0.045 0.175 883 Planarity : 0.004 0.036 968 Dihedral : 8.426 86.727 798 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.63 % Allowed : 16.29 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.81 (0.33), residues: 677 helix: 0.19 (0.92), residues: 32 sheet: -0.72 (0.30), residues: 333 loop : -1.84 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 50 HIS 0.006 0.001 HIS L 190 PHE 0.012 0.001 PHE L 140 TYR 0.010 0.001 TYR A 272 ARG 0.002 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.03069 ( 200) hydrogen bonds : angle 5.83316 ( 543) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.81505 ( 8) covalent geometry : bond 0.00321 ( 5714) covalent geometry : angle 0.54346 ( 7752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7514 (tt) REVERT: H 22 ARG cc_start: 0.7587 (ttt-90) cc_final: 0.7378 (ttt180) REVERT: H 98 TYR cc_start: 0.6315 (OUTLIER) cc_final: 0.4307 (m-80) outliers start: 29 outliers final: 26 residues processed: 94 average time/residue: 0.4533 time to fit residues: 54.9180 Evaluate side-chains 94 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 64 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 190 HIS ** 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 = 0.4428 r_free = 0.4428 target = 0.202912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.185747 restraints weight = 19816.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.189459 restraints weight = 11812.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.191931 restraints weight = 7919.565| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5718 Z= 0.146 Angle : 0.550 5.312 7760 Z= 0.286 Chirality : 0.045 0.173 883 Planarity : 0.004 0.036 968 Dihedral : 8.440 86.522 798 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.79 % Allowed : 17.25 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.33), residues: 677 helix: 1.07 (1.03), residues: 26 sheet: -0.75 (0.30), residues: 333 loop : -1.76 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.012 0.001 HIS L 190 PHE 0.012 0.001 PHE L 140 TYR 0.010 0.001 TYR A 272 ARG 0.002 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 200) hydrogen bonds : angle 5.82649 ( 543) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.83818 ( 8) covalent geometry : bond 0.00326 ( 5714) covalent geometry : angle 0.54940 ( 7752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7537 (tt) REVERT: H 22 ARG cc_start: 0.7599 (ttt-90) cc_final: 0.7384 (ttt180) REVERT: H 98 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.4329 (m-80) outliers start: 30 outliers final: 26 residues processed: 93 average time/residue: 0.3943 time to fit residues: 47.7200 Evaluate side-chains 92 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.201234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.186981 restraints weight = 19687.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.189829 restraints weight = 12691.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.191867 restraints weight = 8879.898| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5718 Z= 0.177 Angle : 0.580 5.877 7760 Z= 0.302 Chirality : 0.045 0.182 883 Planarity : 0.005 0.038 968 Dihedral : 8.567 85.659 798 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 5.27 % Allowed : 17.57 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.93 (0.33), residues: 677 helix: 0.03 (0.90), residues: 32 sheet: -0.87 (0.29), residues: 337 loop : -1.82 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.005 0.001 HIS H 38 PHE 0.013 0.002 PHE L 140 TYR 0.011 0.001 TYR A 272 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 200) hydrogen bonds : angle 6.07332 ( 543) SS BOND : bond 0.00305 ( 4) SS BOND : angle 0.92306 ( 8) covalent geometry : bond 0.00395 ( 5714) covalent geometry : angle 0.57948 ( 7752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.4335 (OUTLIER) cc_final: 0.4095 (p) REVERT: A 171 VAL cc_start: 0.5995 (OUTLIER) cc_final: 0.5714 (m) REVERT: H 21 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7601 (tt) REVERT: H 22 ARG cc_start: 0.7673 (ttt-90) cc_final: 0.7415 (ttt180) REVERT: H 38 HIS cc_start: 0.5636 (OUTLIER) cc_final: 0.5289 (m-70) REVERT: H 98 TYR cc_start: 0.6366 (OUTLIER) cc_final: 0.4383 (m-80) outliers start: 33 outliers final: 26 residues processed: 102 average time/residue: 0.4062 time to fit residues: 54.3391 Evaluate side-chains 99 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.201877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.187761 restraints weight = 19554.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.190421 restraints weight = 12685.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.192424 restraints weight = 8934.594| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5718 Z= 0.158 Angle : 0.565 5.383 7760 Z= 0.292 Chirality : 0.045 0.175 883 Planarity : 0.004 0.038 968 Dihedral : 8.518 85.788 797 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 5.11 % Allowed : 17.41 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.33), residues: 677 helix: 0.12 (0.91), residues: 32 sheet: -0.88 (0.29), residues: 337 loop : -1.84 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.005 0.001 HIS H 219 PHE 0.011 0.002 PHE L 140 TYR 0.011 0.001 TYR A 272 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03197 ( 200) hydrogen bonds : angle 5.98208 ( 543) SS BOND : bond 0.00268 ( 4) SS BOND : angle 0.89573 ( 8) covalent geometry : bond 0.00353 ( 5714) covalent geometry : angle 0.56422 ( 7752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.4400 (OUTLIER) cc_final: 0.4151 (p) REVERT: H 21 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7590 (tt) REVERT: H 22 ARG cc_start: 0.7643 (ttt-90) cc_final: 0.7405 (ttt180) REVERT: H 38 HIS cc_start: 0.5603 (OUTLIER) cc_final: 0.5282 (m-70) REVERT: H 98 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.4405 (m-80) REVERT: H 104 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7507 (mtm) REVERT: L 197 VAL cc_start: 0.5651 (OUTLIER) cc_final: 0.5378 (p) outliers start: 32 outliers final: 25 residues processed: 97 average time/residue: 0.3702 time to fit residues: 46.8710 Evaluate side-chains 97 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 197 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 0.0670 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.202409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.188524 restraints weight = 19620.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.191205 restraints weight = 12572.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.193122 restraints weight = 8806.438| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5718 Z= 0.148 Angle : 0.562 5.353 7760 Z= 0.291 Chirality : 0.045 0.174 883 Planarity : 0.004 0.039 968 Dihedral : 8.481 85.862 797 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.75 % Allowed : 17.41 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.92 (0.33), residues: 677 helix: 0.20 (0.92), residues: 32 sheet: -0.89 (0.29), residues: 337 loop : -1.79 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 PHE 0.021 0.002 PHE A 277 TYR 0.011 0.001 TYR A 272 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 200) hydrogen bonds : angle 5.92718 ( 543) SS BOND : bond 0.00247 ( 4) SS BOND : angle 0.88927 ( 8) covalent geometry : bond 0.00334 ( 5714) covalent geometry : angle 0.56143 ( 7752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 66 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.4507 (OUTLIER) cc_final: 0.4281 (p) REVERT: A 171 VAL cc_start: 0.5973 (OUTLIER) cc_final: 0.5679 (m) REVERT: H 21 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7573 (tt) REVERT: H 38 HIS cc_start: 0.5610 (OUTLIER) cc_final: 0.5272 (m-70) REVERT: H 98 TYR cc_start: 0.6332 (OUTLIER) cc_final: 0.4384 (m-80) REVERT: H 104 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7465 (mtm) REVERT: L 197 VAL cc_start: 0.5625 (OUTLIER) cc_final: 0.5345 (p) outliers start: 36 outliers final: 26 residues processed: 99 average time/residue: 0.3467 time to fit residues: 45.4770 Evaluate side-chains 99 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.200228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.185888 restraints weight = 19629.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.188687 restraints weight = 12616.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.190373 restraints weight = 8954.472| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5718 Z= 0.187 Angle : 0.588 5.791 7760 Z= 0.306 Chirality : 0.046 0.184 883 Planarity : 0.005 0.038 968 Dihedral : 8.468 85.197 796 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 5.75 % Allowed : 17.25 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.05 (0.32), residues: 677 helix: 0.03 (0.93), residues: 30 sheet: -0.96 (0.29), residues: 337 loop : -1.89 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.005 0.001 HIS H 38 PHE 0.017 0.002 PHE A 277 TYR 0.013 0.002 TYR A 272 ARG 0.003 0.000 ARG A 236 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 200) hydrogen bonds : angle 6.17254 ( 543) SS BOND : bond 0.00314 ( 4) SS BOND : angle 1.03593 ( 8) covalent geometry : bond 0.00421 ( 5714) covalent geometry : angle 0.58748 ( 7752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1354 Ramachandran restraints generated. 677 Oldfield, 0 Emsley, 677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.4505 (OUTLIER) cc_final: 0.4258 (p) REVERT: A 171 VAL cc_start: 0.6011 (OUTLIER) cc_final: 0.5718 (m) REVERT: H 21 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7674 (tt) REVERT: H 38 HIS cc_start: 0.5588 (OUTLIER) cc_final: 0.5249 (m-70) REVERT: H 98 TYR cc_start: 0.6383 (OUTLIER) cc_final: 0.4434 (m-80) REVERT: L 197 VAL cc_start: 0.5667 (OUTLIER) cc_final: 0.5388 (p) outliers start: 36 outliers final: 29 residues processed: 100 average time/residue: 0.4670 time to fit residues: 60.8249 Evaluate side-chains 101 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 27 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN H 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.201818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.187587 restraints weight = 19441.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.190275 restraints weight = 12483.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.192172 restraints weight = 8846.224| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5718 Z= 0.143 Angle : 0.562 5.806 7760 Z= 0.292 Chirality : 0.045 0.173 883 Planarity : 0.004 0.038 968 Dihedral : 8.395 85.943 796 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 5.43 % Allowed : 18.21 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.92 (0.33), residues: 677 helix: 0.25 (0.93), residues: 32 sheet: -0.91 (0.29), residues: 337 loop : -1.77 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.004 0.001 HIS A 30 PHE 0.018 0.001 PHE A 277 TYR 0.011 0.001 TYR A 272 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 200) hydrogen bonds : angle 5.92144 ( 543) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.88054 ( 8) covalent geometry : bond 0.00322 ( 5714) covalent geometry : angle 0.56133 ( 7752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4958.56 seconds wall clock time: 89 minutes 23.74 seconds (5363.74 seconds total)