Starting phenix.real_space_refine on Wed May 14 00:23:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tio_41297/05_2025/8tio_41297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tio_41297/05_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_41297/05_2025/8tio_41297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tio_41297/05_2025/8tio_41297.map" model { file = "/net/cci-nas-00/data/ceres_data/8tio_41297/05_2025/8tio_41297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tio_41297/05_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-5687/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: 5.38, per 1000 atoms: 0.48 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: 2.88 Conformation dependent library (CDL) restraints added in 678.3 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: 1.00 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: 3.53 Time building geometry restraints manager: 3.45 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: 1.420 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.240 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.080 ------------------------------------------------------------------------------- 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 : 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: 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: 0.4426 time to fit residues: 77.0420 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 : 0.798 ------------------------------------------------------------------------------- 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: 0.5980 chunk 62 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.202884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.185898 restraints weight = 19575.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.189456 restraints weight = 11682.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.191872 restraints weight = 7868.956| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5718 Z= 0.170 Angle : 0.604 5.641 7760 Z= 0.310 Chirality : 0.046 0.178 883 Planarity : 0.005 0.036 968 Dihedral : 9.110 86.204 810 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 5.11 % Allowed : 13.90 % Favored : 80.99 % 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: -1.87 (0.33), residues: 677 helix: 0.54 (1.03), residues: 24 sheet: -0.82 (0.29), residues: 337 loop : -1.81 (0.35), residues: 316 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 0.013 0.002 PHE L 99 TYR 0.012 0.001 TYR A 272 ARG 0.004 0.001 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 200) hydrogen bonds : angle 6.35249 ( 543) SS BOND : bond 0.00260 ( 4) SS BOND : angle 1.21498 ( 8) covalent geometry : bond 0.00378 ( 5714) covalent geometry : angle 0.60333 ( 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 115 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.807 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 298 THR cc_start: 0.5988 (OUTLIER) cc_final: 0.5732 (p) REVERT: H 21 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7504 (tt) REVERT: H 98 TYR cc_start: 0.6231 (OUTLIER) cc_final: 0.4195 (m-80) outliers start: 32 outliers final: 23 residues processed: 109 average time/residue: 0.3785 time to fit residues: 53.6079 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 : 0.890 ------------------------------------------------------------------------------- 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 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 82 GLU 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: 0.8980 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.0570 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.203202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.186308 restraints weight = 19565.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.189845 restraints weight = 11628.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.192275 restraints weight = 7778.369| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.2421 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= 0.150 Angle : 0.565 5.527 7760 Z= 0.291 Chirality : 0.045 0.175 883 Planarity : 0.004 0.035 968 Dihedral : 8.802 86.346 805 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.79 % Allowed : 15.18 % Favored : 80.03 % 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 (0.32), residues: 677 helix: 0.63 (1.00), residues: 26 sheet: -0.80 (0.29), residues: 335 loop : -1.95 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 PHE 0.013 0.001 PHE L 140 TYR 0.010 0.001 TYR A 272 ARG 0.003 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 200) hydrogen bonds : angle 6.13716 ( 543) SS BOND : bond 0.00259 ( 4) SS BOND : angle 0.96718 ( 8) covalent geometry : bond 0.00334 ( 5714) covalent geometry : angle 0.56480 ( 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 104 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.924 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: 0.5807 (OUTLIER) cc_final: 0.5548 (p) REVERT: H 21 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7521 (tt) REVERT: H 22 ARG cc_start: 0.7592 (ttt-90) cc_final: 0.7376 (ttt180) REVERT: H 98 TYR cc_start: 0.6352 (OUTLIER) cc_final: 0.4362 (m-80) outliers start: 30 outliers final: 25 residues processed: 101 average time/residue: 0.3883 time to fit residues: 51.0270 Evaluate side-chains 98 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.204783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.190720 restraints weight = 19359.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.193526 restraints weight = 12264.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.195267 restraints weight = 8581.086| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.2671 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= 0.120 Angle : 0.534 5.137 7760 Z= 0.276 Chirality : 0.045 0.165 883 Planarity : 0.004 0.035 968 Dihedral : 8.596 86.777 803 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.47 % Allowed : 15.97 % Favored : 79.55 % 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: -1.72 (0.33), residues: 677 helix: 0.92 (1.04), residues: 26 sheet: -0.66 (0.30), residues: 330 loop : -1.80 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.012 0.001 HIS L 190 PHE 0.010 0.001 PHE L 140 TYR 0.009 0.001 TYR H 83 ARG 0.002 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.02964 ( 200) hydrogen bonds : angle 5.86771 ( 543) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.73104 ( 8) covalent geometry : bond 0.00264 ( 5714) covalent geometry : angle 0.53411 ( 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 100 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.815 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: 0.7836 (OUTLIER) cc_final: 0.7533 (tt) REVERT: H 22 ARG cc_start: 0.7486 (ttt-90) cc_final: 0.7150 (ttt180) REVERT: H 98 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.4413 (m-80) outliers start: 28 outliers final: 23 residues processed: 98 average time/residue: 0.3883 time to fit residues: 49.1513 Evaluate side-chains 96 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.0370 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 281 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 = 0.4437 r_free = 0.4437 target = 0.204166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.190604 restraints weight = 19293.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.193325 restraints weight = 12145.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.194878 restraints weight = 8497.404| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5718 Z= 0.134 Angle : 0.538 5.255 7760 Z= 0.278 Chirality : 0.045 0.171 883 Planarity : 0.004 0.036 968 Dihedral : 8.494 86.638 800 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.63 % Allowed : 16.45 % Favored : 78.91 % 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: 0.20 (0.94), residues: 32 sheet: -0.66 (0.30), residues: 330 loop : -1.82 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.006 0.001 HIS L 190 PHE 0.012 0.001 PHE L 140 TYR 0.009 0.001 TYR A 272 ARG 0.002 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 200) hydrogen bonds : angle 5.84699 ( 543) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.78165 ( 8) covalent geometry : bond 0.00300 ( 5714) covalent geometry : angle 0.53772 ( 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 101 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.900 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: 0.7873 (OUTLIER) cc_final: 0.7553 (tt) REVERT: H 22 ARG cc_start: 0.7528 (ttt-90) cc_final: 0.7317 (ttt180) REVERT: H 98 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.4374 (m-80) outliers start: 29 outliers final: 26 residues processed: 98 average time/residue: 0.4061 time to fit residues: 51.2653 Evaluate side-chains 96 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 175 SER 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: 2.9990 chunk 65 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.203345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.188965 restraints weight = 19745.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.191898 restraints weight = 12435.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.193790 restraints weight = 8703.531| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5718 Z= 0.142 Angle : 0.544 5.247 7760 Z= 0.282 Chirality : 0.045 0.173 883 Planarity : 0.004 0.036 968 Dihedral : 8.510 86.447 800 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.63 % Allowed : 18.21 % 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: -1.75 (0.33), residues: 677 helix: 0.20 (0.92), residues: 32 sheet: -0.67 (0.30), residues: 330 loop : -1.80 (0.35), residues: 315 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 0.016 0.001 PHE A 277 TYR 0.009 0.001 TYR A 272 ARG 0.002 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 200) hydrogen bonds : angle 5.87334 ( 543) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.81578 ( 8) covalent geometry : bond 0.00319 ( 5714) covalent geometry : angle 0.54374 ( 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 97 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.912 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: 0.7877 (OUTLIER) cc_final: 0.7552 (tt) REVERT: H 22 ARG cc_start: 0.7575 (ttt-90) cc_final: 0.7365 (ttt180) REVERT: H 98 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.4337 (m-80) outliers start: 29 outliers final: 25 residues processed: 94 average time/residue: 0.4206 time to fit residues: 50.7614 Evaluate side-chains 94 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 347 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 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=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: 0.8980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.202153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.187865 restraints weight = 19574.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.190442 restraints weight = 12562.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.192386 restraints weight = 9112.111| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5718 Z= 0.162 Angle : 0.566 5.482 7760 Z= 0.293 Chirality : 0.045 0.179 883 Planarity : 0.004 0.037 968 Dihedral : 8.569 85.958 800 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 : 4.95 % Allowed : 17.73 % Favored : 77.32 % 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: -1.87 (0.33), residues: 677 helix: 0.17 (0.91), residues: 32 sheet: -0.77 (0.30), residues: 330 loop : -1.85 (0.35), residues: 315 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 0.03171 ( 200) hydrogen bonds : angle 5.99910 ( 543) SS BOND : bond 0.00273 ( 4) SS BOND : angle 0.88199 ( 8) covalent geometry : bond 0.00362 ( 5714) covalent geometry : angle 0.56510 ( 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 104 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.819 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: A 164 VAL cc_start: 0.4456 (OUTLIER) cc_final: 0.4231 (p) REVERT: A 171 VAL cc_start: 0.5978 (OUTLIER) cc_final: 0.5689 (m) REVERT: H 21 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7584 (tt) REVERT: H 22 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.7398 (ttt180) REVERT: H 38 HIS cc_start: 0.5606 (OUTLIER) cc_final: 0.5282 (m-70) REVERT: H 98 TYR cc_start: 0.6352 (OUTLIER) cc_final: 0.4415 (m-80) outliers start: 31 outliers final: 24 residues processed: 101 average time/residue: 0.3884 time to fit residues: 50.4839 Evaluate side-chains 99 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 280 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 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 179 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 67 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.200525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.186193 restraints weight = 19674.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.188917 restraints weight = 12624.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.190827 restraints weight = 8907.962| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.3086 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= 0.185 Angle : 0.586 5.734 7760 Z= 0.305 Chirality : 0.046 0.183 883 Planarity : 0.005 0.038 968 Dihedral : 8.686 85.295 799 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 5.75 % Allowed : 16.93 % Favored : 77.32 % 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: -2.03 (0.33), residues: 677 helix: 0.05 (0.90), residues: 32 sheet: -0.93 (0.29), residues: 337 loop : -1.90 (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 0.012 0.001 TYR A 272 ARG 0.003 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 200) hydrogen bonds : angle 6.16055 ( 543) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.95998 ( 8) covalent geometry : bond 0.00413 ( 5714) covalent geometry : angle 0.58556 ( 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 105 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.925 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: 0.4446 (OUTLIER) cc_final: 0.4207 (p) REVERT: A 171 VAL cc_start: 0.6033 (OUTLIER) cc_final: 0.5750 (m) REVERT: H 21 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7628 (tt) REVERT: H 22 ARG cc_start: 0.7675 (ttt-90) cc_final: 0.7429 (ttt180) REVERT: H 38 HIS cc_start: 0.5589 (OUTLIER) cc_final: 0.5219 (m-70) REVERT: H 98 TYR cc_start: 0.6394 (OUTLIER) cc_final: 0.4428 (m-80) REVERT: H 104 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7484 (mtm) REVERT: L 197 VAL cc_start: 0.5448 (OUTLIER) cc_final: 0.5172 (p) outliers start: 36 outliers final: 27 residues processed: 102 average time/residue: 0.3914 time to fit residues: 52.0007 Evaluate side-chains 104 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 251 CYS 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 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 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=1.50 ------------------------------------------------------------------------------- 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: 0.5980 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.202448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.185801 restraints weight = 19632.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.189385 restraints weight = 11725.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.191848 restraints weight = 7805.056| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5718 Z= 0.149 Angle : 0.563 5.320 7760 Z= 0.292 Chirality : 0.045 0.173 883 Planarity : 0.004 0.038 968 Dihedral : 8.492 85.845 798 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 5.91 % Allowed : 16.77 % Favored : 77.32 % 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: -1.91 (0.33), residues: 677 helix: 0.25 (0.93), residues: 32 sheet: -0.82 (0.29), residues: 331 loop : -1.88 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 PHE 0.011 0.001 PHE A 277 TYR 0.011 0.001 TYR A 272 ARG 0.002 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 200) hydrogen bonds : angle 5.95217 ( 543) SS BOND : bond 0.00243 ( 4) SS BOND : angle 0.87990 ( 8) covalent geometry : bond 0.00333 ( 5714) covalent geometry : angle 0.56295 ( 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 107 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 0.817 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: A 164 VAL cc_start: 0.4682 (OUTLIER) cc_final: 0.4388 (p) REVERT: A 171 VAL cc_start: 0.5981 (OUTLIER) cc_final: 0.5684 (m) REVERT: H 21 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7567 (tt) REVERT: H 22 ARG cc_start: 0.7616 (ttt-90) cc_final: 0.7294 (ttt180) REVERT: H 38 HIS cc_start: 0.5615 (OUTLIER) cc_final: 0.5266 (m-70) REVERT: H 98 TYR cc_start: 0.6349 (OUTLIER) cc_final: 0.4386 (m-80) REVERT: H 104 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7497 (mtm) outliers start: 37 outliers final: 29 residues processed: 103 average time/residue: 0.3823 time to fit residues: 51.6784 Evaluate side-chains 103 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 280 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 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 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 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 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.201245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.187078 restraints weight = 19569.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.189820 restraints weight = 12534.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.191751 restraints weight = 8865.902| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5718 Z= 0.154 Angle : 0.562 5.379 7760 Z= 0.290 Chirality : 0.045 0.178 883 Planarity : 0.004 0.039 968 Dihedral : 8.490 85.727 798 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.75 % Allowed : 17.09 % 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: -1.94 (0.33), residues: 677 helix: 0.29 (0.96), residues: 30 sheet: -0.88 (0.29), residues: 331 loop : -1.83 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 50 HIS 0.005 0.001 HIS H 38 PHE 0.012 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 0.03137 ( 200) hydrogen bonds : angle 5.96407 ( 543) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.91967 ( 8) covalent geometry : bond 0.00347 ( 5714) covalent geometry : angle 0.56172 ( 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 103 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 0.816 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: 0.4652 (OUTLIER) cc_final: 0.4378 (p) REVERT: A 171 VAL cc_start: 0.5994 (OUTLIER) cc_final: 0.5686 (m) REVERT: H 21 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7602 (tt) REVERT: H 22 ARG cc_start: 0.7643 (ttt-90) cc_final: 0.7373 (ttt180) REVERT: H 38 HIS cc_start: 0.5524 (OUTLIER) cc_final: 0.5193 (m-70) REVERT: H 98 TYR cc_start: 0.6346 (OUTLIER) cc_final: 0.4405 (m-80) outliers start: 36 outliers final: 30 residues processed: 100 average time/residue: 0.3821 time to fit residues: 49.9925 Evaluate side-chains 102 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 280 ASN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 315 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 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 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 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: 0.7980 chunk 45 optimal weight: 0.0000 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.0470 chunk 8 optimal weight: 2.9990 overall best weight: 0.3882 ------------------------------------------------------------------------------- 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 = 0.4436 r_free = 0.4436 target = 0.204244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.190515 restraints weight = 19352.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.193260 restraints weight = 12180.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.194850 restraints weight = 8504.336| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.3366 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= 0.113 Angle : 0.535 5.697 7760 Z= 0.275 Chirality : 0.045 0.165 883 Planarity : 0.004 0.038 968 Dihedral : 8.315 86.861 798 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.79 % Allowed : 18.53 % Favored : 76.68 % 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: -1.80 (0.33), residues: 677 helix: 0.57 (0.97), residues: 32 sheet: -0.90 (0.29), residues: 340 loop : -1.64 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 50 HIS 0.004 0.001 HIS A 30 PHE 0.012 0.001 PHE A 277 TYR 0.010 0.001 TYR A 272 ARG 0.002 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.02778 ( 200) hydrogen bonds : angle 5.64831 ( 543) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.80492 ( 8) covalent geometry : bond 0.00255 ( 5714) covalent geometry : angle 0.53493 ( 7752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4491.42 seconds wall clock time: 78 minutes 12.41 seconds (4692.41 seconds total)