Starting phenix.real_space_refine on Tue Feb 11 17:11:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fjb_29221/02_2025/8fjb_29221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fjb_29221/02_2025/8fjb_29221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fjb_29221/02_2025/8fjb_29221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fjb_29221/02_2025/8fjb_29221.map" model { file = "/net/cci-nas-00/data/ceres_data/8fjb_29221/02_2025/8fjb_29221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fjb_29221/02_2025/8fjb_29221.cif" } resolution = 3.06 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= 1.000 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 24 5.16 5 C 3980 2.51 5 N 1095 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6330 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2230 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "E" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1555 Classifications: {'peptide': 207} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Time building chain proxies: 4.72, per 1000 atoms: 0.75 Number of scatterers: 6330 At special positions: 0 Unit cell: (139.4, 107.1, 72.25, 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 24 16.00 O 1231 8.00 N 1095 7.00 C 3980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 201 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 893.7 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 17 sheets defined 14.2% alpha, 46.9% 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 56 through 85 removed outlier: 3.773A pdb=" N TRP A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 151 removed outlier: 3.559A pdb=" N LYS A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.656A pdb=" N GLU E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 190 through 197 removed outlier: 3.682A pdb=" N THR E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.991A pdb=" N SER D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 190 removed outlier: 3.818A pdb=" N HIS D 190 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.752A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 111 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS A 114 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA A 125 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR A 116 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 194 removed outlier: 5.740A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 194 removed outlier: 5.740A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.814A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.814A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.030A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.892A pdb=" N VAL E 107 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.278A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.278A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.543A pdb=" N LYS E 214 " --> pdb=" O CYS E 201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.283A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N GLN D 27 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N SER D 67 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 11.757A pdb=" N ILE D 29 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 11.586A pdb=" N SER D 65 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.775A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.555A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 154 through 155 326 hydrogen bonds defined for protein. 852 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: 1.95 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2070 1.34 - 1.46: 1646 1.46 - 1.58: 2739 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 6489 Sorted by residual: bond pdb=" CG GLN D 90 " pdb=" CD GLN D 90 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.14e+00 bond pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 1.506 1.455 0.051 3.90e-02 6.57e+02 1.74e+00 bond pdb=" CG ARG A 6 " pdb=" CD ARG A 6 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" CG ASP A 137 " pdb=" OD1 ASP A 137 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.69e+00 bond pdb=" CB ASP A 137 " pdb=" CG ASP A 137 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.64e+00 ... (remaining 6484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 8625 2.04 - 4.08: 168 4.08 - 6.13: 11 6.13 - 8.17: 5 8.17 - 10.21: 2 Bond angle restraints: 8811 Sorted by residual: angle pdb=" C SER D 93 " pdb=" N THR D 94 " pdb=" CA THR D 94 " ideal model delta sigma weight residual 121.80 132.01 -10.21 2.44e+00 1.68e-01 1.75e+01 angle pdb=" N ASP A 196 " pdb=" CA ASP A 196 " pdb=" C ASP A 196 " ideal model delta sigma weight residual 111.28 114.81 -3.53 1.09e+00 8.42e-01 1.05e+01 angle pdb=" C VAL A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta sigma weight residual 121.53 128.72 -7.19 2.25e+00 1.98e-01 1.02e+01 angle pdb=" C TYR D 92 " pdb=" N SER D 93 " pdb=" CA SER D 93 " ideal model delta sigma weight residual 121.54 115.81 5.73 1.91e+00 2.74e-01 9.01e+00 angle pdb=" C ASP A 137 " pdb=" CA ASP A 137 " pdb=" CB ASP A 137 " ideal model delta sigma weight residual 110.45 116.23 -5.78 2.15e+00 2.16e-01 7.22e+00 ... (remaining 8806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3557 17.89 - 35.79: 245 35.79 - 53.68: 40 53.68 - 71.58: 14 71.58 - 89.47: 6 Dihedral angle restraints: 3862 sinusoidal: 1533 harmonic: 2329 Sorted by residual: dihedral pdb=" CA THR D 94 " pdb=" C THR D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta harmonic sigma weight residual 0.00 -25.14 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ILE D 29 " pdb=" C ILE D 29 " pdb=" N SER D 30 " pdb=" CA SER D 30 " ideal model delta harmonic sigma weight residual -180.00 -161.95 -18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" C ASP A 137 " pdb=" N ASP A 137 " pdb=" CA ASP A 137 " pdb=" CB ASP A 137 " ideal model delta harmonic sigma weight residual -122.60 -131.62 9.02 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 3859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 824 0.068 - 0.137: 114 0.137 - 0.205: 9 0.205 - 0.274: 1 0.274 - 0.342: 1 Chirality restraints: 949 Sorted by residual: chirality pdb=" CB ILE B 1 " pdb=" CA ILE B 1 " pdb=" CG1 ILE B 1 " pdb=" CG2 ILE B 1 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA ASP A 137 " pdb=" N ASP A 137 " pdb=" C ASP A 137 " pdb=" CB ASP A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE D 97 " pdb=" N ILE D 97 " pdb=" C ILE D 97 " pdb=" CB ILE D 97 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 946 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 95 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO D 96 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 96 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 96 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 194 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C VAL A 194 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL A 194 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 195 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO D 95 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " 0.021 5.00e-02 4.00e+02 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 132 2.69 - 3.24: 5410 3.24 - 3.79: 8981 3.79 - 4.35: 12444 4.35 - 4.90: 22199 Nonbonded interactions: 49166 Sorted by model distance: nonbonded pdb=" OE1 GLU D 188 " pdb=" NH1 ARG D 212 " model vdw 2.135 3.120 nonbonded pdb=" OG1 THR E 200 " pdb=" O LYS E 214 " model vdw 2.257 3.040 nonbonded pdb=" OG SER D 14 " pdb=" OD2 ASP D 17 " model vdw 2.270 3.040 nonbonded pdb=" O LEU D 126 " pdb=" NZ LYS D 184 " model vdw 2.291 3.120 nonbonded pdb=" OE1 GLU C 4 " pdb=" OH TYR E 32 " model vdw 2.296 3.040 ... (remaining 49161 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.630 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6489 Z= 0.390 Angle : 0.683 10.209 8811 Z= 0.362 Chirality : 0.049 0.342 949 Planarity : 0.005 0.065 1138 Dihedral : 13.228 89.472 2347 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.66 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.28), residues: 788 helix: -0.94 (0.47), residues: 96 sheet: 0.03 (0.28), residues: 330 loop : -1.97 (0.28), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 244 HIS 0.005 0.001 HIS C 5 PHE 0.029 0.002 PHE B 70 TYR 0.024 0.002 TYR E 33 ARG 0.008 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.698 Fit side-chains REVERT: B 19 LYS cc_start: 0.8774 (mmtt) cc_final: 0.7978 (mtpp) REVERT: B 34 ASP cc_start: 0.8409 (m-30) cc_final: 0.8206 (m-30) REVERT: B 38 ASP cc_start: 0.8283 (m-30) cc_final: 0.7975 (m-30) REVERT: D 82 ASP cc_start: 0.8671 (m-30) cc_final: 0.8433 (m-30) REVERT: D 144 GLU cc_start: 0.8558 (mp0) cc_final: 0.8344 (mp0) REVERT: D 190 HIS cc_start: 0.8933 (m90) cc_final: 0.8649 (m90) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2943 time to fit residues: 31.4862 Evaluate side-chains 82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 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 = 0.3435 r_free = 0.3435 target = 0.111552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.071582 restraints weight = 9354.537| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.97 r_work: 0.2621 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6489 Z= 0.225 Angle : 0.560 11.694 8811 Z= 0.291 Chirality : 0.044 0.221 949 Planarity : 0.005 0.053 1138 Dihedral : 4.398 18.327 881 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.29 % Allowed : 4.75 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.29), residues: 788 helix: 0.24 (0.52), residues: 98 sheet: 0.67 (0.28), residues: 349 loop : -1.22 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS B 51 PHE 0.014 0.001 PHE B 70 TYR 0.017 0.001 TYR E 33 ARG 0.011 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.749 Fit side-chains REVERT: A 108 ARG cc_start: 0.8318 (mmm-85) cc_final: 0.8086 (mmm160) REVERT: A 173 GLU cc_start: 0.8710 (tp30) cc_final: 0.8066 (mt-10) REVERT: A 176 LYS cc_start: 0.8364 (ttpp) cc_final: 0.8150 (ptmm) REVERT: B 19 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8029 (mtpp) REVERT: B 34 ASP cc_start: 0.8864 (m-30) cc_final: 0.8637 (m-30) REVERT: B 38 ASP cc_start: 0.8598 (m-30) cc_final: 0.8323 (m-30) REVERT: D 159 ASN cc_start: 0.8841 (p0) cc_final: 0.8462 (p0) REVERT: D 190 HIS cc_start: 0.8771 (m90) cc_final: 0.8473 (m90) outliers start: 2 outliers final: 2 residues processed: 87 average time/residue: 0.2604 time to fit residues: 28.5186 Evaluate side-chains 83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN E 202 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.068837 restraints weight = 9435.631| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.96 r_work: 0.2570 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 6489 Z= 0.392 Angle : 0.607 12.796 8811 Z= 0.313 Chirality : 0.046 0.189 949 Planarity : 0.005 0.050 1138 Dihedral : 4.588 22.176 881 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.72 % Allowed : 7.19 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.29), residues: 788 helix: 0.38 (0.51), residues: 98 sheet: 0.92 (0.27), residues: 359 loop : -1.07 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.004 0.001 HIS C 5 PHE 0.016 0.002 PHE D 140 TYR 0.018 0.002 TYR E 33 ARG 0.009 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.780 Fit side-chains REVERT: B 19 LYS cc_start: 0.8783 (mmtt) cc_final: 0.7978 (mtpp) REVERT: B 34 ASP cc_start: 0.8878 (m-30) cc_final: 0.8671 (m-30) REVERT: B 38 ASP cc_start: 0.8700 (m-30) cc_final: 0.8451 (m-30) REVERT: D 159 ASN cc_start: 0.8853 (p0) cc_final: 0.8511 (p0) REVERT: D 188 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8655 (mm-30) REVERT: D 190 HIS cc_start: 0.8912 (m90) cc_final: 0.8470 (m90) REVERT: D 212 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7881 (ttp80) outliers start: 5 outliers final: 4 residues processed: 87 average time/residue: 0.2611 time to fit residues: 28.3259 Evaluate side-chains 85 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 19 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 76 optimal weight: 0.0170 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN E 77 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.071194 restraints weight = 9476.636| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.93 r_work: 0.2634 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6489 Z= 0.178 Angle : 0.509 11.330 8811 Z= 0.264 Chirality : 0.042 0.156 949 Planarity : 0.004 0.050 1138 Dihedral : 4.191 19.700 881 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.72 % Allowed : 8.78 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.30), residues: 788 helix: 0.83 (0.54), residues: 98 sheet: 1.35 (0.28), residues: 340 loop : -0.87 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.002 0.000 HIS B 51 PHE 0.009 0.001 PHE A 33 TYR 0.014 0.001 TYR E 33 ARG 0.004 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.672 Fit side-chains REVERT: A 89 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8249 (mp0) REVERT: A 108 ARG cc_start: 0.8356 (mmm-85) cc_final: 0.8097 (mmm160) REVERT: A 173 GLU cc_start: 0.8772 (tp30) cc_final: 0.8141 (mt-10) REVERT: A 253 GLN cc_start: 0.8284 (mt0) cc_final: 0.7550 (pm20) REVERT: B 19 LYS cc_start: 0.8746 (mmtt) cc_final: 0.7972 (mtpp) REVERT: B 34 ASP cc_start: 0.8829 (m-30) cc_final: 0.8617 (m-30) REVERT: D 24 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7843 (ttm-80) REVERT: D 159 ASN cc_start: 0.8822 (p0) cc_final: 0.8508 (p0) REVERT: D 188 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8619 (mm-30) REVERT: D 190 HIS cc_start: 0.8827 (m90) cc_final: 0.8386 (m90) REVERT: D 212 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7869 (ttp80) outliers start: 5 outliers final: 3 residues processed: 83 average time/residue: 0.2727 time to fit residues: 28.0228 Evaluate side-chains 80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.0370 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 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 = 0.3448 r_free = 0.3448 target = 0.112687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.072386 restraints weight = 9360.147| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.01 r_work: 0.2631 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6489 Z= 0.184 Angle : 0.504 11.229 8811 Z= 0.259 Chirality : 0.042 0.138 949 Planarity : 0.004 0.049 1138 Dihedral : 4.047 18.038 881 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.86 % Allowed : 9.50 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.30), residues: 788 helix: 1.03 (0.53), residues: 98 sheet: 1.53 (0.29), residues: 339 loop : -0.62 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.002 0.001 HIS B 51 PHE 0.010 0.001 PHE A 33 TYR 0.014 0.001 TYR E 33 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.748 Fit side-chains REVERT: A 108 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.8074 (mmm160) REVERT: A 173 GLU cc_start: 0.8767 (tp30) cc_final: 0.8150 (mt-10) REVERT: A 253 GLN cc_start: 0.8374 (mt0) cc_final: 0.8123 (pt0) REVERT: B 19 LYS cc_start: 0.8712 (mmtt) cc_final: 0.7936 (mtpp) REVERT: B 34 ASP cc_start: 0.8888 (m-30) cc_final: 0.8671 (m-30) REVERT: E 199 TYR cc_start: 0.7435 (m-80) cc_final: 0.7062 (m-80) REVERT: D 159 ASN cc_start: 0.8821 (p0) cc_final: 0.8478 (p0) REVERT: D 188 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8643 (mm-30) REVERT: D 190 HIS cc_start: 0.8852 (m90) cc_final: 0.8491 (m90) REVERT: D 212 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7613 (ttp-170) outliers start: 6 outliers final: 5 residues processed: 84 average time/residue: 0.2558 time to fit residues: 26.9746 Evaluate side-chains 82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.068025 restraints weight = 9396.474| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.92 r_work: 0.2675 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 6489 Z= 0.324 Angle : 0.560 12.317 8811 Z= 0.286 Chirality : 0.044 0.159 949 Planarity : 0.004 0.047 1138 Dihedral : 4.297 21.486 881 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.15 % Allowed : 9.50 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.30), residues: 788 helix: 0.86 (0.52), residues: 98 sheet: 1.57 (0.28), residues: 343 loop : -0.52 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS C 5 PHE 0.013 0.002 PHE D 140 TYR 0.016 0.002 TYR E 33 ARG 0.006 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.725 Fit side-chains REVERT: A 108 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.8119 (mmm160) REVERT: A 173 GLU cc_start: 0.8816 (tp30) cc_final: 0.8273 (mt-10) REVERT: A 253 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8215 (pt0) REVERT: B 19 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8093 (mtpp) REVERT: B 34 ASP cc_start: 0.8884 (m-30) cc_final: 0.8674 (m-30) REVERT: D 159 ASN cc_start: 0.8923 (p0) cc_final: 0.8570 (p0) REVERT: D 188 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8650 (mm-30) REVERT: D 190 HIS cc_start: 0.8914 (m90) cc_final: 0.8510 (m90) REVERT: D 212 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7720 (ttp-170) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.2548 time to fit residues: 25.1572 Evaluate side-chains 80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 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 = 0.3473 r_free = 0.3473 target = 0.113004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.073236 restraints weight = 9577.545| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.84 r_work: 0.2691 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6489 Z= 0.196 Angle : 0.509 11.284 8811 Z= 0.261 Chirality : 0.042 0.136 949 Planarity : 0.004 0.046 1138 Dihedral : 4.104 20.182 881 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.01 % Allowed : 9.78 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.30), residues: 788 helix: 1.02 (0.52), residues: 98 sheet: 1.61 (0.29), residues: 344 loop : -0.46 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.002 0.001 HIS B 51 PHE 0.010 0.001 PHE A 33 TYR 0.014 0.001 TYR E 33 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.739 Fit side-chains REVERT: A 108 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.8193 (mmm160) REVERT: A 173 GLU cc_start: 0.8800 (tp30) cc_final: 0.8289 (mt-10) REVERT: A 253 GLN cc_start: 0.8442 (mt0) cc_final: 0.8217 (pt0) REVERT: B 19 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8092 (mtpp) REVERT: E 199 TYR cc_start: 0.7505 (m-80) cc_final: 0.7173 (m-80) REVERT: D 159 ASN cc_start: 0.8916 (p0) cc_final: 0.8589 (p0) REVERT: D 188 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8664 (mm-30) REVERT: D 190 HIS cc_start: 0.8887 (m90) cc_final: 0.8492 (m90) REVERT: D 212 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7719 (ttp-170) outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.2556 time to fit residues: 25.6366 Evaluate side-chains 78 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain D residue 7 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 36 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.108027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.068769 restraints weight = 9368.847| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.90 r_work: 0.2701 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6489 Z= 0.264 Angle : 0.535 11.824 8811 Z= 0.273 Chirality : 0.043 0.148 949 Planarity : 0.004 0.046 1138 Dihedral : 4.186 21.397 881 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.72 % Allowed : 10.79 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.30), residues: 788 helix: 0.95 (0.52), residues: 98 sheet: 1.65 (0.29), residues: 343 loop : -0.41 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.002 0.001 HIS B 51 PHE 0.011 0.001 PHE D 140 TYR 0.015 0.001 TYR E 33 ARG 0.005 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.726 Fit side-chains REVERT: A 108 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.8145 (mmm160) REVERT: A 173 GLU cc_start: 0.8763 (tp30) cc_final: 0.8220 (mt-10) REVERT: A 253 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: B 19 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8023 (mtpp) REVERT: D 159 ASN cc_start: 0.8933 (p0) cc_final: 0.8560 (p0) REVERT: D 188 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8636 (mm-30) REVERT: D 190 HIS cc_start: 0.8910 (m90) cc_final: 0.8458 (m90) REVERT: D 212 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7734 (ttp80) outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 0.2587 time to fit residues: 25.3726 Evaluate side-chains 80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain D residue 7 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.067302 restraints weight = 9476.548| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.84 r_work: 0.2648 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6489 Z= 0.325 Angle : 0.561 12.357 8811 Z= 0.286 Chirality : 0.044 0.156 949 Planarity : 0.004 0.045 1138 Dihedral : 4.320 24.154 881 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.72 % Allowed : 11.51 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.30), residues: 788 helix: 0.89 (0.52), residues: 98 sheet: 1.62 (0.28), residues: 343 loop : -0.43 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS C 5 PHE 0.013 0.002 PHE D 140 TYR 0.016 0.002 TYR E 33 ARG 0.005 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.610 Fit side-chains REVERT: A 108 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8202 (mmm160) REVERT: B 19 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8094 (mtpp) REVERT: B 75 LYS cc_start: 0.8470 (mmtt) cc_final: 0.7889 (mtmm) REVERT: D 159 ASN cc_start: 0.8986 (p0) cc_final: 0.8645 (p0) REVERT: D 188 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8652 (mm-30) REVERT: D 212 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7781 (ttp80) outliers start: 5 outliers final: 4 residues processed: 81 average time/residue: 0.2551 time to fit residues: 25.7072 Evaluate side-chains 79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain D residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.107768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.069151 restraints weight = 9419.953| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.84 r_work: 0.2680 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6489 Z= 0.201 Angle : 0.515 11.564 8811 Z= 0.263 Chirality : 0.042 0.136 949 Planarity : 0.004 0.046 1138 Dihedral : 4.122 21.954 881 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.58 % Allowed : 11.94 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.30), residues: 788 helix: 1.06 (0.52), residues: 98 sheet: 1.65 (0.29), residues: 342 loop : -0.26 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 244 HIS 0.003 0.001 HIS D 190 PHE 0.009 0.001 PHE A 33 TYR 0.015 0.001 TYR E 33 ARG 0.003 0.000 ARG A 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.712 Fit side-chains REVERT: A 108 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.8197 (mmm160) REVERT: A 173 GLU cc_start: 0.8762 (tp30) cc_final: 0.8248 (mt-10) REVERT: A 253 GLN cc_start: 0.8395 (pt0) cc_final: 0.7744 (pm20) REVERT: B 19 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8090 (mtpp) REVERT: B 75 LYS cc_start: 0.8489 (mmtt) cc_final: 0.7886 (mtmm) REVERT: E 211 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8429 (mmmm) REVERT: D 159 ASN cc_start: 0.8972 (p0) cc_final: 0.8643 (p0) REVERT: D 188 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8661 (mm-30) REVERT: D 190 HIS cc_start: 0.8935 (m90) cc_final: 0.8699 (m-70) REVERT: D 212 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7765 (ttp-170) outliers start: 4 outliers final: 4 residues processed: 79 average time/residue: 0.2615 time to fit residues: 25.7926 Evaluate side-chains 80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain D residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 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 = 0.3466 r_free = 0.3466 target = 0.111413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.073745 restraints weight = 9623.162| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.72 r_work: 0.2679 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6489 Z= 0.244 Angle : 0.532 11.677 8811 Z= 0.271 Chirality : 0.043 0.145 949 Planarity : 0.004 0.045 1138 Dihedral : 4.145 21.883 881 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.58 % Allowed : 12.37 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.30), residues: 788 helix: 1.04 (0.52), residues: 98 sheet: 1.61 (0.28), residues: 343 loop : -0.30 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.003 0.001 HIS D 190 PHE 0.010 0.001 PHE A 33 TYR 0.015 0.001 TYR E 33 ARG 0.004 0.000 ARG A 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4182.07 seconds wall clock time: 74 minutes 59.39 seconds (4499.39 seconds total)