Starting phenix.real_space_refine on Sat Aug 23 09:29:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tio_41297/08_2025/8tio_41297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tio_41297/08_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_41297/08_2025/8tio_41297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tio_41297/08_2025/8tio_41297.map" model { file = "/net/cci-nas-00/data/ceres_data/8tio_41297/08_2025/8tio_41297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tio_41297/08_2025/8tio_41297.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.01, per 1000 atoms: 0.18 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: 1.19 Conformation dependent library (CDL) restraints added in 203.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 2.06 Time building geometry restraints manager: 1.58 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: 3.000 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: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.410 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.790 ------------------------------------------------------------------------------- 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 : 13.80 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 236 TYR 0.009 0.001 TYR A 272 PHE 0.010 0.001 PHE L 140 TRP 0.011 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 5714) covalent geometry : angle 0.62069 ( 7752) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.79930 ( 8) hydrogen bonds : bond 0.13001 ( 200) hydrogen bonds : angle 7.20601 ( 543) *********************** 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 : 0.184 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 54 TYR cc_start: 0.3739 (m-80) cc_final: 0.3365 (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: 0.7436 (tt) REVERT: H 98 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.4255 (m-80) outliers start: 30 outliers final: 19 residues processed: 140 average time/residue: 0.1917 time to fit residues: 33.6920 Evaluate side-chains 96 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 173 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0020 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.4451 r_free = 0.4451 target = 0.205297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.188366 restraints weight = 19567.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.192113 restraints weight = 11492.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.194628 restraints weight = 7619.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.196263 restraints weight = 5478.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.197067 restraints weight = 4313.283| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5843 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5718 Z= 0.129 Angle : 0.569 5.870 7760 Z= 0.290 Chirality : 0.045 0.164 883 Planarity : 0.004 0.035 968 Dihedral : 8.816 87.089 808 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.15 % Allowed : 14.54 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.33), residues: 677 helix: 0.68 (1.03), residues: 24 sheet: -0.73 (0.29), residues: 338 loop : -1.73 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.011 0.001 TYR A 272 PHE 0.013 0.001 PHE L 99 TRP 0.012 0.001 TRP H 50 HIS 0.006 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5714) covalent geometry : angle 0.56858 ( 7752) SS BOND : bond 0.00179 ( 4) SS BOND : angle 1.01058 ( 8) hydrogen bonds : bond 0.03285 ( 200) hydrogen bonds : angle 6.09940 ( 543) *********************** 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 103 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.324 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: 0.5785 (OUTLIER) cc_final: 0.5526 (p) REVERT: H 21 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7491 (tt) REVERT: H 22 ARG cc_start: 0.7383 (ttt-90) cc_final: 0.7164 (ttt180) REVERT: H 98 TYR cc_start: 0.6219 (OUTLIER) cc_final: 0.4268 (m-80) outliers start: 26 outliers final: 20 residues processed: 99 average time/residue: 0.1985 time to fit residues: 25.1935 Evaluate side-chains 95 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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 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 55 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.201635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.184460 restraints weight = 19760.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.188148 restraints weight = 11804.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.190327 restraints weight = 7893.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.192047 restraints weight = 5860.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.193226 restraints weight = 4617.052| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.2405 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= 0.182 Angle : 0.591 6.151 7760 Z= 0.306 Chirality : 0.046 0.185 883 Planarity : 0.005 0.035 968 Dihedral : 8.777 85.986 802 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 4.79 % Allowed : 14.54 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.32), residues: 677 helix: 0.52 (0.99), residues: 26 sheet: -0.78 (0.29), residues: 332 loop : -1.91 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.012 0.001 TYR A 272 PHE 0.015 0.002 PHE L 140 TRP 0.011 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 5714) covalent geometry : angle 0.59055 ( 7752) SS BOND : bond 0.00334 ( 4) SS BOND : angle 1.11506 ( 8) hydrogen bonds : bond 0.03585 ( 200) hydrogen bonds : angle 6.22943 ( 543) *********************** 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: 30 poor density : 75 time to evaluate : 0.205 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: H 21 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7477 (tt) REVERT: H 98 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.4302 (m-80) outliers start: 30 outliers final: 26 residues processed: 103 average time/residue: 0.1840 time to fit residues: 24.6864 Evaluate side-chains 95 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 6 GLN 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 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 27 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.203586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.189402 restraints weight = 19531.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.192195 restraints weight = 12393.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.194111 restraints weight = 8687.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.195094 restraints weight = 6607.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.196060 restraints weight = 5483.436| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.2669 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= 0.134 Angle : 0.553 5.212 7760 Z= 0.285 Chirality : 0.045 0.169 883 Planarity : 0.004 0.034 968 Dihedral : 8.642 86.546 802 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.79 % Allowed : 16.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.33), residues: 677 helix: 0.85 (1.04), residues: 26 sheet: -0.70 (0.30), residues: 329 loop : -1.83 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.009 0.001 TYR H 83 PHE 0.011 0.001 PHE L 140 TRP 0.012 0.001 TRP H 50 HIS 0.010 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 5714) covalent geometry : angle 0.55249 ( 7752) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.84738 ( 8) hydrogen bonds : bond 0.03113 ( 200) hydrogen bonds : angle 5.96104 ( 543) *********************** 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: 30 poor density : 66 time to evaluate : 0.229 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: H 21 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7438 (tt) REVERT: H 22 ARG cc_start: 0.7602 (ttt-90) cc_final: 0.7399 (ttt180) REVERT: H 98 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.4390 (m-80) outliers start: 30 outliers final: 24 residues processed: 94 average time/residue: 0.1968 time to fit residues: 23.7464 Evaluate side-chains 91 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 6 GLN 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 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 65 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.0170 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 overall best weight: 0.4620 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.205115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.191486 restraints weight = 19284.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.194229 restraints weight = 12084.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.195757 restraints weight = 8374.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.197290 restraints weight = 6495.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.197907 restraints weight = 5142.332| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.2834 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= 0.117 Angle : 0.528 5.085 7760 Z= 0.272 Chirality : 0.045 0.165 883 Planarity : 0.004 0.034 968 Dihedral : 8.488 87.014 800 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.95 % Allowed : 16.45 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.33), residues: 677 helix: 1.19 (1.09), residues: 26 sheet: -0.63 (0.30), residues: 329 loop : -1.73 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.008 0.001 TYR A 272 PHE 0.010 0.001 PHE L 140 TRP 0.012 0.001 TRP H 50 HIS 0.012 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5714) covalent geometry : angle 0.52756 ( 7752) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.76580 ( 8) hydrogen bonds : bond 0.02927 ( 200) hydrogen bonds : angle 5.71904 ( 543) *********************** 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: 31 poor density : 70 time to evaluate : 0.285 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: H 22 ARG cc_start: 0.7610 (ttt-90) cc_final: 0.7141 (ttt180) REVERT: H 98 TYR cc_start: 0.6287 (OUTLIER) cc_final: 0.4388 (m-80) outliers start: 31 outliers final: 27 residues processed: 97 average time/residue: 0.2005 time to fit residues: 24.6079 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 : 0.321 ------------------------------------------------------------------------------- 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 6 GLN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4442 r_free = 0.4442 target = 0.204465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.190760 restraints weight = 19675.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.193564 restraints weight = 12448.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.195328 restraints weight = 8610.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.196704 restraints weight = 6516.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.197375 restraints weight = 5250.019| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.2973 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= 0.124 Angle : 0.531 5.172 7760 Z= 0.274 Chirality : 0.045 0.166 883 Planarity : 0.004 0.034 968 Dihedral : 8.188 87.053 796 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.95 % Allowed : 17.25 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.33), residues: 677 helix: 1.25 (1.08), residues: 26 sheet: -0.67 (0.30), residues: 334 loop : -1.69 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.008 0.001 TYR A 272 PHE 0.017 0.001 PHE A 277 TRP 0.011 0.001 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5714) covalent geometry : angle 0.53029 ( 7752) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.78153 ( 8) hydrogen bonds : bond 0.02896 ( 200) hydrogen bonds : angle 5.67494 ( 543) *********************** 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: 31 poor density : 66 time to evaluate : 0.303 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 164 VAL cc_start: 0.4774 (OUTLIER) cc_final: 0.4475 (p) REVERT: H 22 ARG cc_start: 0.7577 (ttt-90) cc_final: 0.7298 (ttt180) REVERT: H 98 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.4376 (m-80) outliers start: 31 outliers final: 27 residues processed: 94 average time/residue: 0.2113 time to fit residues: 25.2565 Evaluate side-chains 91 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 347 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 6 GLN 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 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 41 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN H 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.203039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.189239 restraints weight = 19692.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.191995 restraints weight = 12537.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.193891 restraints weight = 8782.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.194766 restraints weight = 6607.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.195752 restraints weight = 5546.665| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.3031 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= 0.153 Angle : 0.558 5.343 7760 Z= 0.288 Chirality : 0.045 0.174 883 Planarity : 0.004 0.035 968 Dihedral : 8.250 86.454 796 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 5.11 % Allowed : 17.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.33), residues: 677 helix: 0.21 (0.96), residues: 32 sheet: -0.78 (0.29), residues: 340 loop : -1.65 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.010 0.001 TYR A 272 PHE 0.024 0.002 PHE A 277 TRP 0.010 0.002 TRP H 50 HIS 0.006 0.001 HIS H 219 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 5714) covalent geometry : angle 0.55748 ( 7752) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.87594 ( 8) hydrogen bonds : bond 0.03118 ( 200) hydrogen bonds : angle 5.77762 ( 543) *********************** 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 97 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.342 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: A 164 VAL cc_start: 0.4733 (OUTLIER) cc_final: 0.4473 (p) REVERT: H 22 ARG cc_start: 0.7591 (ttt-90) cc_final: 0.7219 (ttt180) REVERT: H 98 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.4332 (m-80) outliers start: 32 outliers final: 28 residues processed: 93 average time/residue: 0.2069 time to fit residues: 24.4054 Evaluate side-chains 94 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 280 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 347 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain H residue 6 GLN 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 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 22 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4426 r_free = 0.4426 target = 0.202721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.188797 restraints weight = 19596.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.191580 restraints weight = 12475.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.193482 restraints weight = 8714.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.194793 restraints weight = 6553.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.195387 restraints weight = 5275.728| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.3116 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= 0.146 Angle : 0.550 5.308 7760 Z= 0.284 Chirality : 0.045 0.172 883 Planarity : 0.004 0.037 968 Dihedral : 8.253 86.548 796 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.95 % Allowed : 17.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.33), residues: 677 helix: 1.24 (1.05), residues: 26 sheet: -0.78 (0.29), residues: 340 loop : -1.58 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.009 0.001 TYR A 272 PHE 0.017 0.002 PHE A 277 TRP 0.011 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5714) covalent geometry : angle 0.54948 ( 7752) SS BOND : bond 0.00253 ( 4) SS BOND : angle 0.88876 ( 8) hydrogen bonds : bond 0.03239 ( 200) hydrogen bonds : angle 5.83333 ( 543) *********************** 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 98 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.344 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 164 VAL cc_start: 0.4686 (OUTLIER) cc_final: 0.4437 (p) REVERT: A 171 VAL cc_start: 0.5925 (OUTLIER) cc_final: 0.5600 (m) REVERT: H 22 ARG cc_start: 0.7588 (ttt-90) cc_final: 0.7148 (ttt180) REVERT: H 38 HIS cc_start: 0.5575 (OUTLIER) cc_final: 0.5369 (m-70) REVERT: H 98 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.4327 (m-80) outliers start: 31 outliers final: 24 residues processed: 95 average time/residue: 0.1982 time to fit residues: 24.3621 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 : 0.265 ------------------------------------------------------------------------------- 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 280 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 353 HIS Chi-restraints excluded: chain H residue 6 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4426 r_free = 0.4426 target = 0.202902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.189325 restraints weight = 19580.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.192113 restraints weight = 12390.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.194159 restraints weight = 8499.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.195140 restraints weight = 6069.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.195398 restraints weight = 5119.378| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.3227 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= 0.147 Angle : 0.558 5.444 7760 Z= 0.289 Chirality : 0.045 0.172 883 Planarity : 0.004 0.035 968 Dihedral : 8.108 86.472 794 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.34), residues: 677 helix: 1.30 (1.06), residues: 26 sheet: -0.86 (0.29), residues: 347 loop : -1.51 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 62 TYR 0.010 0.001 TYR A 272 PHE 0.015 0.002 PHE A 277 TRP 0.011 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5714) covalent geometry : angle 0.55718 ( 7752) SS BOND : bond 0.00253 ( 4) SS BOND : angle 0.87653 ( 8) hydrogen bonds : bond 0.03085 ( 200) hydrogen bonds : angle 5.77108 ( 543) *********************** 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 98 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.240 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 164 VAL cc_start: 0.4712 (OUTLIER) cc_final: 0.4428 (p) REVERT: A 171 VAL cc_start: 0.5951 (OUTLIER) cc_final: 0.5599 (m) REVERT: H 22 ARG cc_start: 0.7515 (ttt-90) cc_final: 0.7294 (ttt180) REVERT: H 98 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.4314 (m-80) outliers start: 30 outliers final: 24 residues processed: 95 average time/residue: 0.1889 time to fit residues: 23.0733 Evaluate side-chains 92 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 280 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 353 HIS Chi-restraints excluded: chain H residue 6 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.0170 chunk 39 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 0.0370 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.3034 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.206459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.193332 restraints weight = 19620.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.195794 restraints weight = 12437.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.197845 restraints weight = 8589.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.198772 restraints weight = 6160.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.200104 restraints weight = 5231.980| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5718 Z= 0.100 Angle : 0.513 4.718 7760 Z= 0.261 Chirality : 0.044 0.158 883 Planarity : 0.004 0.035 968 Dihedral : 7.884 87.874 794 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.67 % Allowed : 19.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.34), residues: 677 helix: 1.62 (1.09), residues: 26 sheet: -0.77 (0.29), residues: 348 loop : -1.35 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.010 0.001 TYR A 321 PHE 0.014 0.001 PHE A 277 TRP 0.015 0.001 TRP H 50 HIS 0.008 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 5714) covalent geometry : angle 0.51255 ( 7752) SS BOND : bond 0.00203 ( 4) SS BOND : angle 0.73744 ( 8) hydrogen bonds : bond 0.02677 ( 200) hydrogen bonds : angle 5.36390 ( 543) ********************** 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 90 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.317 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: H 22 ARG cc_start: 0.7477 (ttt-90) cc_final: 0.7158 (ttt180) REVERT: H 98 TYR cc_start: 0.6183 (OUTLIER) cc_final: 0.4299 (m-80) REVERT: L 139 ASN cc_start: 0.5379 (m-40) cc_final: 0.4670 (p0) REVERT: L 179 THR cc_start: 0.6581 (OUTLIER) cc_final: 0.6260 (m) outliers start: 23 outliers final: 19 residues processed: 87 average time/residue: 0.2109 time to fit residues: 23.4021 Evaluate side-chains 87 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 6 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 57 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4445 r_free = 0.4445 target = 0.205005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.191510 restraints weight = 19555.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.194463 restraints weight = 12041.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.196232 restraints weight = 8045.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.197085 restraints weight = 5853.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.198378 restraints weight = 5084.769| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 moved from start: 0.3502 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= 0.124 Angle : 0.541 5.526 7760 Z= 0.277 Chirality : 0.045 0.168 883 Planarity : 0.004 0.033 968 Dihedral : 7.802 87.517 792 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.67 % Allowed : 19.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.34), residues: 677 helix: 1.49 (1.07), residues: 26 sheet: -0.82 (0.29), residues: 350 loop : -1.35 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.009 0.001 TYR H 116 PHE 0.012 0.001 PHE L 140 TRP 0.011 0.001 TRP H 50 HIS 0.007 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 5714) covalent geometry : angle 0.54026 ( 7752) SS BOND : bond 0.00205 ( 4) SS BOND : angle 0.78708 ( 8) hydrogen bonds : bond 0.02802 ( 200) hydrogen bonds : angle 5.39908 ( 543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2551.69 seconds wall clock time: 44 minutes 9.29 seconds (2649.29 seconds total)