Starting phenix.real_space_refine on Tue Mar 11 19:41:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vuz_43545/03_2025/8vuz_43545.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vuz_43545/03_2025/8vuz_43545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vuz_43545/03_2025/8vuz_43545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vuz_43545/03_2025/8vuz_43545.map" model { file = "/net/cci-nas-00/data/ceres_data/8vuz_43545/03_2025/8vuz_43545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vuz_43545/03_2025/8vuz_43545.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4166 2.51 5 N 1114 2.21 5 O 1323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6626 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1652 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain: "B" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1696 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Chain: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1590 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Time building chain proxies: 4.32, per 1000 atoms: 0.65 Number of scatterers: 6626 At special positions: 0 Unit cell: (59.76, 67.23, 158.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1323 8.00 N 1114 7.00 C 4166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 141 " - pdb=" SG CYS H 197 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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: 1.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 20 sheets defined 7.0% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.629A pdb=" N GLU A 64 " --> pdb=" O GLN A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.762A pdb=" N SER A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.868A pdb=" N LEU B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.778A pdb=" N THR B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.663A pdb=" N LYS H 64 " --> pdb=" O GLU H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 98 through 100B removed outlier: 3.639A pdb=" N GLY H 100A" --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 193 removed outlier: 3.954A pdb=" N THR H 192 " --> pdb=" O SER H 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.911A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.616A pdb=" N VAL A 18 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.282A pdb=" N GLU A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.536A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 177 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 144 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR A 175 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.536A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 177 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 144 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR A 175 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 154 removed outlier: 7.007A pdb=" N VAL A 193 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 210 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 195 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.741A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.606A pdb=" N GLY B 84 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 37 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.990A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 134 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 178 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.990A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 139 " --> pdb=" O TYR B 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.720A pdb=" N ASN B 145 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 193 " --> pdb=" O LYS B 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.705A pdb=" N TRP H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 120 through 123 removed outlier: 5.968A pdb=" N TYR H 177 " --> pdb=" O ASP H 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 138 through 139 Processing sheet with id=AB7, first strand: chain 'H' and resid 152 through 155 Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 14 removed outlier: 7.148A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.082A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 145 through 150 removed outlier: 3.666A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 630 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: 2.05 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.95: 1 0.95 - 1.20: 0 1.20 - 1.45: 3014 1.45 - 1.70: 3736 1.70 - 1.95: 29 Bond restraints: 6780 Sorted by residual: bond pdb=" CG PRO L 119 " pdb=" CD PRO L 119 " ideal model delta sigma weight residual 1.503 0.703 0.800 3.40e-02 8.65e+02 5.53e+02 bond pdb=" CB PRO L 119 " pdb=" CG PRO L 119 " ideal model delta sigma weight residual 1.492 1.947 -0.455 5.00e-02 4.00e+02 8.28e+01 bond pdb=" N PRO L 119 " pdb=" CD PRO L 119 " ideal model delta sigma weight residual 1.473 1.599 -0.126 1.40e-02 5.10e+03 8.08e+01 bond pdb=" N PRO L 119 " pdb=" CA PRO L 119 " ideal model delta sigma weight residual 1.465 1.322 0.143 2.03e-02 2.43e+03 4.93e+01 bond pdb=" CB PRO H 214 " pdb=" CG PRO H 214 " ideal model delta sigma weight residual 1.492 1.632 -0.140 5.00e-02 4.00e+02 7.87e+00 ... (remaining 6775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.21: 9217 5.21 - 10.42: 14 10.42 - 15.63: 1 15.63 - 20.84: 1 20.84 - 26.05: 2 Bond angle restraints: 9235 Sorted by residual: angle pdb=" N PRO L 119 " pdb=" CD PRO L 119 " pdb=" CG PRO L 119 " ideal model delta sigma weight residual 103.20 77.15 26.05 1.50e+00 4.44e-01 3.01e+02 angle pdb=" CA PRO L 119 " pdb=" CB PRO L 119 " pdb=" CG PRO L 119 " ideal model delta sigma weight residual 104.50 83.94 20.56 1.90e+00 2.77e-01 1.17e+02 angle pdb=" CA PRO L 119 " pdb=" N PRO L 119 " pdb=" CD PRO L 119 " ideal model delta sigma weight residual 112.00 96.85 15.15 1.40e+00 5.10e-01 1.17e+02 angle pdb=" N PRO L 119 " pdb=" CA PRO L 119 " pdb=" CB PRO L 119 " ideal model delta sigma weight residual 103.08 95.32 7.76 9.70e-01 1.06e+00 6.40e+01 angle pdb=" CB PRO L 119 " pdb=" CG PRO L 119 " pdb=" CD PRO L 119 " ideal model delta sigma weight residual 106.10 83.74 22.36 3.20e+00 9.77e-02 4.88e+01 ... (remaining 9230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 3424 17.78 - 35.56: 505 35.56 - 53.33: 111 53.33 - 71.11: 18 71.11 - 88.89: 10 Dihedral angle restraints: 4068 sinusoidal: 1545 harmonic: 2523 Sorted by residual: dihedral pdb=" CB CYS H 141 " pdb=" SG CYS H 141 " pdb=" SG CYS H 197 " pdb=" CB CYS H 197 " ideal model delta sinusoidal sigma weight residual 93.00 162.64 -69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CA LYS B 50 " pdb=" C LYS B 50 " pdb=" N VAL B 51 " pdb=" CA VAL B 51 " ideal model delta harmonic sigma weight residual -180.00 -144.17 -35.83 0 5.00e+00 4.00e-02 5.13e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 195 " pdb=" CB CYS A 195 " ideal model delta sinusoidal sigma weight residual 93.00 145.51 -52.51 1 1.00e+01 1.00e-02 3.76e+01 ... (remaining 4065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 808 0.045 - 0.090: 171 0.090 - 0.135: 79 0.135 - 0.180: 0 0.180 - 0.224: 1 Chirality restraints: 1059 Sorted by residual: chirality pdb=" CA PRO L 119 " pdb=" N PRO L 119 " pdb=" C PRO L 119 " pdb=" CB PRO L 119 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA PRO B 141 " pdb=" N PRO B 141 " pdb=" C PRO B 141 " pdb=" CB PRO B 141 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA TYR B 140 " pdb=" N TYR B 140 " pdb=" C TYR B 140 " pdb=" CB TYR B 140 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1056 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE L 118 " -0.097 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO L 119 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO L 119 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO L 119 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 213 " -0.093 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO H 214 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO H 214 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO H 214 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO L 59 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.022 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 108 2.62 - 3.19: 5850 3.19 - 3.76: 10027 3.76 - 4.33: 13368 4.33 - 4.90: 22129 Nonbonded interactions: 51482 Sorted by model distance: nonbonded pdb=" OG1 THR B 182 " pdb=" OD1 ASP B 184 " model vdw 2.050 3.040 nonbonded pdb=" OE1 GLN L 166 " pdb=" OG SER L 171 " model vdw 2.140 3.040 nonbonded pdb=" OG SER B 201 " pdb=" O SER B 203 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN A 52 " pdb=" OH TYR L 32 " model vdw 2.234 3.040 nonbonded pdb=" N GLU H 149 " pdb=" OE1 GLU H 149 " model vdw 2.240 3.120 ... (remaining 51477 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.430 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.012 0.800 6780 Z= 0.886 Angle : 0.809 26.045 9235 Z= 0.433 Chirality : 0.044 0.224 1059 Planarity : 0.007 0.135 1175 Dihedral : 17.378 88.887 2422 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.75 % Favored : 93.13 % Rotamer: Outliers : 0.13 % Allowed : 35.97 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.30), residues: 859 helix: -1.40 (0.75), residues: 36 sheet: 0.44 (0.26), residues: 407 loop : -0.55 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 148 HIS 0.005 0.001 HIS B 198 PHE 0.013 0.002 PHE L 118 TYR 0.020 0.001 TYR L 140 ARG 0.004 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8321 (mppt) cc_final: 0.7921 (mmpt) REVERT: B 149 LYS cc_start: 0.7403 (tttm) cc_final: 0.6937 (tptp) outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.1794 time to fit residues: 36.3759 Evaluate side-chains 147 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110391 restraints weight = 9645.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108771 restraints weight = 7302.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.110036 restraints weight = 5500.328| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6780 Z= 0.231 Angle : 0.657 10.328 9235 Z= 0.339 Chirality : 0.044 0.157 1059 Planarity : 0.005 0.076 1175 Dihedral : 4.988 38.485 929 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.22 % Allowed : 32.28 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.30), residues: 859 helix: -1.62 (0.70), residues: 38 sheet: 0.72 (0.26), residues: 416 loop : -0.62 (0.34), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 148 HIS 0.004 0.001 HIS B 198 PHE 0.019 0.002 PHE B 135 TYR 0.015 0.001 TYR B 140 ARG 0.004 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASN cc_start: 0.9179 (t0) cc_final: 0.8960 (t0) REVERT: A 115 LYS cc_start: 0.8294 (mppt) cc_final: 0.8007 (mmtt) REVERT: B 148 TRP cc_start: 0.8266 (m100) cc_final: 0.7949 (m100) REVERT: H 72 ASP cc_start: 0.8148 (t0) cc_final: 0.7672 (t0) outliers start: 32 outliers final: 18 residues processed: 186 average time/residue: 0.1884 time to fit residues: 46.2193 Evaluate side-chains 160 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 69 optimal weight: 0.0170 chunk 43 optimal weight: 0.0470 chunk 49 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114586 restraints weight = 9574.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110460 restraints weight = 7527.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112274 restraints weight = 6738.830| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6780 Z= 0.167 Angle : 0.625 7.457 9235 Z= 0.317 Chirality : 0.044 0.152 1059 Planarity : 0.005 0.059 1175 Dihedral : 4.736 37.496 927 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.53 % Allowed : 31.62 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.30), residues: 859 helix: -1.64 (0.73), residues: 38 sheet: 0.81 (0.25), residues: 418 loop : -0.61 (0.34), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 148 HIS 0.003 0.001 HIS A 35 PHE 0.013 0.002 PHE B 135 TYR 0.015 0.001 TYR B 140 ARG 0.005 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8323 (mppt) cc_final: 0.8041 (mmtt) REVERT: A 205 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8738 (mtmm) REVERT: B 105 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: B 108 ARG cc_start: 0.7529 (ptm-80) cc_final: 0.7318 (ptm-80) REVERT: B 145 ASN cc_start: 0.7642 (t0) cc_final: 0.7334 (t0) REVERT: B 148 TRP cc_start: 0.8330 (m100) cc_final: 0.7821 (m100) REVERT: L 3 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: L 82 ASP cc_start: 0.7711 (m-30) cc_final: 0.7392 (m-30) REVERT: L 118 PHE cc_start: 0.8833 (m-80) cc_final: 0.8622 (m-80) REVERT: L 136 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8280 (pp) outliers start: 42 outliers final: 25 residues processed: 185 average time/residue: 0.1854 time to fit residues: 45.1369 Evaluate side-chains 168 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 43 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112797 restraints weight = 9730.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110206 restraints weight = 6985.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111655 restraints weight = 6244.621| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6780 Z= 0.204 Angle : 0.627 7.691 9235 Z= 0.317 Chirality : 0.043 0.151 1059 Planarity : 0.004 0.052 1175 Dihedral : 4.704 37.418 927 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 6.46 % Allowed : 30.43 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.30), residues: 859 helix: -1.86 (0.74), residues: 38 sheet: 0.87 (0.26), residues: 419 loop : -0.60 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.003 0.001 HIS B 198 PHE 0.025 0.002 PHE L 139 TYR 0.012 0.001 TYR B 140 ARG 0.004 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8327 (mppt) cc_final: 0.8019 (mmtt) REVERT: A 205 LYS cc_start: 0.8975 (mtmm) cc_final: 0.8742 (mtmm) REVERT: B 105 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7525 (pm20) REVERT: B 145 ASN cc_start: 0.7587 (t0) cc_final: 0.7276 (t0) REVERT: B 170 ASP cc_start: 0.8585 (t0) cc_final: 0.8375 (t0) REVERT: H 38 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8360 (ptt90) REVERT: H 72 ASP cc_start: 0.8277 (t0) cc_final: 0.8001 (t0) REVERT: L 3 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: L 119 PRO cc_start: 0.8924 (Cg_endo) cc_final: 0.8717 (Cg_exo) REVERT: L 136 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8275 (pp) outliers start: 49 outliers final: 28 residues processed: 187 average time/residue: 0.1845 time to fit residues: 45.5125 Evaluate side-chains 174 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN L 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110953 restraints weight = 9688.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109724 restraints weight = 6398.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110938 restraints weight = 6392.087| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6780 Z= 0.220 Angle : 0.635 7.884 9235 Z= 0.320 Chirality : 0.043 0.146 1059 Planarity : 0.005 0.049 1175 Dihedral : 4.692 37.530 927 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 6.46 % Allowed : 31.23 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.30), residues: 859 helix: -1.86 (0.75), residues: 38 sheet: 0.92 (0.26), residues: 408 loop : -0.48 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 148 HIS 0.003 0.001 HIS B 198 PHE 0.015 0.001 PHE B 135 TYR 0.012 0.001 TYR B 140 ARG 0.004 0.000 ARG A 82B *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.8563 (t0) cc_final: 0.8216 (t70) REVERT: A 95 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8459 (tt) REVERT: A 115 LYS cc_start: 0.8355 (mppt) cc_final: 0.8053 (mmtt) REVERT: A 205 LYS cc_start: 0.8965 (mtmm) cc_final: 0.8759 (mtmm) REVERT: B 105 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: B 145 ASN cc_start: 0.7572 (t0) cc_final: 0.7369 (t0) REVERT: H 38 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8548 (ptt90) REVERT: L 3 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: L 61 ARG cc_start: 0.8300 (ptt90) cc_final: 0.7807 (ptt90) REVERT: L 82 ASP cc_start: 0.7746 (m-30) cc_final: 0.7266 (m-30) REVERT: L 119 PRO cc_start: 0.8953 (Cg_endo) cc_final: 0.8739 (Cg_exo) REVERT: L 136 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8270 (pp) outliers start: 49 outliers final: 30 residues processed: 189 average time/residue: 0.1746 time to fit residues: 43.7847 Evaluate side-chains 173 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109541 restraints weight = 9521.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107787 restraints weight = 7720.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.109367 restraints weight = 6848.797| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6780 Z= 0.226 Angle : 0.642 7.958 9235 Z= 0.327 Chirality : 0.043 0.147 1059 Planarity : 0.005 0.045 1175 Dihedral : 4.749 37.506 927 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.93 % Allowed : 31.23 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.30), residues: 859 helix: -1.78 (0.76), residues: 38 sheet: 0.91 (0.26), residues: 406 loop : -0.49 (0.33), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 148 HIS 0.003 0.001 HIS B 198 PHE 0.016 0.001 PHE B 135 TYR 0.012 0.001 TYR B 140 ARG 0.013 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.8342 (t0) cc_final: 0.7983 (t70) REVERT: B 211 ARG cc_start: 0.5543 (mmm-85) cc_final: 0.4957 (mtp85) REVERT: H 38 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8686 (ptt90) REVERT: L 3 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: L 35 TRP cc_start: 0.8418 (OUTLIER) cc_final: 0.7959 (m-90) REVERT: L 61 ARG cc_start: 0.8208 (ptt90) cc_final: 0.7723 (ptt90) REVERT: L 82 ASP cc_start: 0.7786 (m-30) cc_final: 0.7209 (m-30) outliers start: 45 outliers final: 32 residues processed: 177 average time/residue: 0.1926 time to fit residues: 44.2832 Evaluate side-chains 172 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 0.0070 chunk 21 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108782 restraints weight = 9636.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109828 restraints weight = 6202.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110840 restraints weight = 5196.611| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6780 Z= 0.225 Angle : 0.662 12.711 9235 Z= 0.331 Chirality : 0.043 0.144 1059 Planarity : 0.005 0.043 1175 Dihedral : 4.767 37.603 927 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 6.46 % Allowed : 30.43 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.30), residues: 859 helix: -1.67 (0.78), residues: 38 sheet: 0.92 (0.26), residues: 407 loop : -0.55 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 148 HIS 0.003 0.001 HIS B 198 PHE 0.015 0.002 PHE B 135 TYR 0.015 0.001 TYR B 140 ARG 0.007 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 53 TYR cc_start: 0.8818 (t80) cc_final: 0.8492 (t80) REVERT: A 86 ASP cc_start: 0.8630 (t0) cc_final: 0.8237 (t70) REVERT: B 185 GLU cc_start: 0.7267 (pm20) cc_final: 0.7060 (pm20) REVERT: B 211 ARG cc_start: 0.5503 (mmm-85) cc_final: 0.4912 (mtp85) REVERT: H 38 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8521 (ptt90) REVERT: H 117 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7076 (pptt) REVERT: L 3 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7874 (mt0) REVERT: L 35 TRP cc_start: 0.8415 (OUTLIER) cc_final: 0.7833 (m-90) REVERT: L 61 ARG cc_start: 0.8297 (ptt90) cc_final: 0.7660 (ptt90) REVERT: L 82 ASP cc_start: 0.7869 (m-30) cc_final: 0.7238 (m-30) outliers start: 49 outliers final: 37 residues processed: 182 average time/residue: 0.1909 time to fit residues: 45.6598 Evaluate side-chains 179 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.0470 chunk 43 optimal weight: 0.6980 overall best weight: 0.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.156491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110937 restraints weight = 9764.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110727 restraints weight = 5498.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111675 restraints weight = 4287.011| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6780 Z= 0.183 Angle : 0.673 11.836 9235 Z= 0.333 Chirality : 0.044 0.144 1059 Planarity : 0.004 0.044 1175 Dihedral : 4.719 36.591 927 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.67 % Allowed : 31.49 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 859 helix: -1.71 (0.77), residues: 38 sheet: 1.01 (0.26), residues: 403 loop : -0.52 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 148 HIS 0.002 0.001 HIS B 198 PHE 0.024 0.002 PHE L 139 TYR 0.015 0.001 TYR L 173 ARG 0.006 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 53 TYR cc_start: 0.8674 (t80) cc_final: 0.8397 (t80) REVERT: A 86 ASP cc_start: 0.8406 (t0) cc_final: 0.8018 (t70) REVERT: A 115 LYS cc_start: 0.8197 (mmpt) cc_final: 0.7639 (mppt) REVERT: B 6 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: B 108 ARG cc_start: 0.7849 (ptm-80) cc_final: 0.7536 (ptm-80) REVERT: B 170 ASP cc_start: 0.8763 (t0) cc_final: 0.8399 (t0) REVERT: H 38 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8575 (ptt90) REVERT: H 72 ASP cc_start: 0.8232 (t0) cc_final: 0.7990 (t0) REVERT: H 117 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6981 (pptt) REVERT: H 179 LEU cc_start: 0.9245 (pt) cc_final: 0.8691 (pp) REVERT: L 3 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: L 35 TRP cc_start: 0.8396 (OUTLIER) cc_final: 0.7852 (m-90) REVERT: L 36 TYR cc_start: 0.8913 (m-10) cc_final: 0.8292 (m-10) REVERT: L 61 ARG cc_start: 0.8273 (ptt90) cc_final: 0.7673 (ptt90) REVERT: L 82 ASP cc_start: 0.7772 (m-30) cc_final: 0.7127 (m-30) outliers start: 43 outliers final: 29 residues processed: 174 average time/residue: 0.1998 time to fit residues: 45.8886 Evaluate side-chains 170 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.154980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109599 restraints weight = 9752.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108723 restraints weight = 6018.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110324 restraints weight = 4832.496| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6780 Z= 0.204 Angle : 0.696 10.494 9235 Z= 0.345 Chirality : 0.044 0.141 1059 Planarity : 0.004 0.043 1175 Dihedral : 4.684 36.058 927 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.48 % Allowed : 33.20 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 859 helix: -1.70 (0.78), residues: 38 sheet: 1.00 (0.26), residues: 403 loop : -0.50 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 148 HIS 0.002 0.001 HIS B 198 PHE 0.022 0.002 PHE B 135 TYR 0.013 0.001 TYR B 140 ARG 0.007 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.8766 (t80) cc_final: 0.8520 (t80) REVERT: A 86 ASP cc_start: 0.8550 (t0) cc_final: 0.8161 (t70) REVERT: A 115 LYS cc_start: 0.8247 (mmpt) cc_final: 0.7640 (mppt) REVERT: A 143 LYS cc_start: 0.7533 (mmmm) cc_final: 0.7198 (mmmt) REVERT: B 6 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: B 108 ARG cc_start: 0.7954 (ptm-80) cc_final: 0.7626 (ptm-80) REVERT: B 155 ARG cc_start: 0.7844 (ptp90) cc_final: 0.7594 (ptp90) REVERT: B 170 ASP cc_start: 0.8809 (t0) cc_final: 0.8455 (t0) REVERT: B 211 ARG cc_start: 0.5500 (mmm-85) cc_final: 0.4905 (mtp85) REVERT: H 38 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8490 (ptt90) REVERT: H 117 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6981 (pptt) REVERT: H 179 LEU cc_start: 0.9260 (pt) cc_final: 0.8696 (pp) REVERT: L 3 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: L 24 ARG cc_start: 0.8752 (ttm-80) cc_final: 0.8348 (ttm-80) REVERT: L 35 TRP cc_start: 0.8393 (OUTLIER) cc_final: 0.7831 (m-90) REVERT: L 61 ARG cc_start: 0.8299 (ptt90) cc_final: 0.7646 (ptt90) REVERT: L 82 ASP cc_start: 0.7795 (m-30) cc_final: 0.7142 (m-30) outliers start: 34 outliers final: 28 residues processed: 169 average time/residue: 0.1982 time to fit residues: 43.5827 Evaluate side-chains 172 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.155240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112545 restraints weight = 9880.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108776 restraints weight = 6620.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110547 restraints weight = 5428.943| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6780 Z= 0.224 Angle : 0.696 10.518 9235 Z= 0.345 Chirality : 0.044 0.141 1059 Planarity : 0.004 0.043 1175 Dihedral : 4.699 36.076 927 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.48 % Allowed : 32.81 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.30), residues: 859 helix: -1.67 (0.79), residues: 38 sheet: 0.97 (0.26), residues: 405 loop : -0.52 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 148 HIS 0.003 0.001 HIS B 198 PHE 0.024 0.002 PHE B 135 TYR 0.013 0.001 TYR B 140 ARG 0.006 0.000 ARG B 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.8767 (t80) cc_final: 0.8532 (t80) REVERT: A 86 ASP cc_start: 0.8480 (t0) cc_final: 0.8083 (t70) REVERT: A 115 LYS cc_start: 0.8210 (mmpt) cc_final: 0.7640 (mppt) REVERT: A 143 LYS cc_start: 0.7583 (mmmm) cc_final: 0.7256 (mmmt) REVERT: B 108 ARG cc_start: 0.7883 (ptm-80) cc_final: 0.7647 (ptm-80) REVERT: B 170 ASP cc_start: 0.8723 (t0) cc_final: 0.8425 (t0) REVERT: B 211 ARG cc_start: 0.5530 (mmm-85) cc_final: 0.4943 (mtp85) REVERT: H 38 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8543 (ptt90) REVERT: H 117 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6925 (pptt) REVERT: H 179 LEU cc_start: 0.9261 (pt) cc_final: 0.8674 (pp) REVERT: L 3 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: L 24 ARG cc_start: 0.8799 (ttm-80) cc_final: 0.8428 (ttm-80) REVERT: L 35 TRP cc_start: 0.8418 (OUTLIER) cc_final: 0.7905 (m-90) REVERT: L 61 ARG cc_start: 0.8276 (ptt90) cc_final: 0.7615 (ptt90) REVERT: L 82 ASP cc_start: 0.7813 (m-30) cc_final: 0.7135 (m-30) outliers start: 34 outliers final: 28 residues processed: 172 average time/residue: 0.1942 time to fit residues: 43.5192 Evaluate side-chains 174 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 22 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112083 restraints weight = 9714.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107953 restraints weight = 6914.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109684 restraints weight = 5867.538| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6780 Z= 0.215 Angle : 0.694 10.440 9235 Z= 0.346 Chirality : 0.044 0.142 1059 Planarity : 0.004 0.043 1175 Dihedral : 4.696 35.946 927 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.35 % Allowed : 33.07 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.30), residues: 859 helix: -1.65 (0.79), residues: 38 sheet: 1.01 (0.26), residues: 405 loop : -0.52 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 148 HIS 0.003 0.001 HIS B 198 PHE 0.022 0.002 PHE B 135 TYR 0.012 0.001 TYR B 140 ARG 0.007 0.000 ARG B 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2233.46 seconds wall clock time: 39 minutes 54.89 seconds (2394.89 seconds total)