Starting phenix.real_space_refine on Thu Jun 5 14:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fjb_29221/06_2025/8fjb_29221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fjb_29221/06_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_29221/06_2025/8fjb_29221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fjb_29221/06_2025/8fjb_29221.map" model { file = "/net/cci-nas-00/data/ceres_data/8fjb_29221/06_2025/8fjb_29221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fjb_29221/06_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-5710/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: 5.23, per 1000 atoms: 0.83 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: 1.32 Conformation dependent library (CDL) restraints added in 977.9 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: 1.08 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: 2.10 Time building geometry restraints manager: 1.63 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: 3.900 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.310 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- 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 6496 Z= 0.239 Angle : 0.685 10.209 8825 Z= 0.363 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 Details of bonding type rmsd hydrogen bonds : bond 0.23165 ( 278) hydrogen bonds : angle 8.99180 ( 852) SS BOND : bond 0.00562 ( 7) SS BOND : angle 1.39339 ( 14) covalent geometry : bond 0.00584 ( 6489) covalent geometry : angle 0.68320 ( 8811) *********************** 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 : 0.689 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: 0.2865 time to fit residues: 30.6517 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 : 0.734 ------------------------------------------------------------------------------- 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: 0.8980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.111072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.071235 restraints weight = 9349.151| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.95 r_work: 0.2614 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6496 Z= 0.147 Angle : 0.566 11.565 8825 Z= 0.294 Chirality : 0.044 0.230 949 Planarity : 0.005 0.053 1138 Dihedral : 4.415 17.688 881 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.29 % Allowed : 4.60 % Favored : 95.11 % 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: -0.35 (0.29), residues: 788 helix: 0.19 (0.52), residues: 98 sheet: 0.57 (0.27), residues: 363 loop : -1.27 (0.31), residues: 327 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 0.013 0.002 PHE B 70 TYR 0.017 0.001 TYR E 33 ARG 0.008 0.001 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 278) hydrogen bonds : angle 5.76180 ( 852) SS BOND : bond 0.00615 ( 7) SS BOND : angle 1.10683 ( 14) covalent geometry : bond 0.00343 ( 6489) covalent geometry : angle 0.56499 ( 8811) *********************** 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 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 1.119 Fit side-chains REVERT: A 108 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.8086 (mmm160) REVERT: B 19 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8023 (mtpp) REVERT: B 34 ASP cc_start: 0.8870 (m-30) cc_final: 0.8651 (m-30) REVERT: B 38 ASP cc_start: 0.8604 (m-30) cc_final: 0.8326 (m-30) REVERT: D 159 ASN cc_start: 0.8834 (p0) cc_final: 0.8448 (p0) REVERT: D 190 HIS cc_start: 0.8779 (m90) cc_final: 0.8469 (m90) outliers start: 2 outliers final: 2 residues processed: 88 average time/residue: 0.3669 time to fit residues: 40.6706 Evaluate side-chains 84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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: 0.2980 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 66 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: 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 = 0.3401 r_free = 0.3401 target = 0.109467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.069978 restraints weight = 9409.187| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.91 r_work: 0.2613 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6496 Z= 0.158 Angle : 0.549 12.056 8825 Z= 0.283 Chirality : 0.044 0.184 949 Planarity : 0.004 0.051 1138 Dihedral : 4.309 18.053 881 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.72 % Allowed : 7.05 % Favored : 92.23 % 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: 0.27 (0.29), residues: 788 helix: 0.65 (0.52), residues: 98 sheet: 1.11 (0.28), residues: 347 loop : -0.95 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS C 5 PHE 0.013 0.001 PHE B 70 TYR 0.017 0.001 TYR E 33 ARG 0.008 0.001 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 278) hydrogen bonds : angle 5.20508 ( 852) SS BOND : bond 0.00571 ( 7) SS BOND : angle 1.10684 ( 14) covalent geometry : bond 0.00381 ( 6489) covalent geometry : angle 0.54733 ( 8811) *********************** 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 85 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.738 Fit side-chains REVERT: A 108 ARG cc_start: 0.8406 (mmm-85) cc_final: 0.8180 (mmm160) REVERT: A 173 GLU cc_start: 0.8766 (tp30) cc_final: 0.8179 (mt-10) REVERT: B 19 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8048 (mtpp) REVERT: B 34 ASP cc_start: 0.8862 (m-30) cc_final: 0.8660 (m-30) REVERT: B 38 ASP cc_start: 0.8600 (m-30) cc_final: 0.8349 (m-30) REVERT: D 159 ASN cc_start: 0.8815 (p0) cc_final: 0.8514 (p0) REVERT: D 188 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8594 (mm-30) REVERT: D 190 HIS cc_start: 0.8908 (m90) cc_final: 0.8445 (m90) REVERT: D 212 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7750 (ttp80) outliers start: 5 outliers final: 5 residues processed: 83 average time/residue: 0.2761 time to fit residues: 28.4566 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 : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET 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: 10.0000 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 30 optimal weight: 0.0070 chunk 7 optimal weight: 1.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** 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 = 0.3395 r_free = 0.3395 target = 0.109101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.069565 restraints weight = 9505.399| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.92 r_work: 0.2604 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6496 Z= 0.173 Angle : 0.547 12.295 8825 Z= 0.281 Chirality : 0.044 0.163 949 Planarity : 0.004 0.049 1138 Dihedral : 4.316 20.090 881 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.01 % Allowed : 7.77 % Favored : 91.22 % 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: 0.56 (0.30), residues: 788 helix: 0.84 (0.54), residues: 98 sheet: 1.36 (0.28), residues: 340 loop : -0.78 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.003 0.001 HIS C 5 PHE 0.011 0.002 PHE D 140 TYR 0.016 0.001 TYR E 33 ARG 0.006 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 278) hydrogen bonds : angle 5.04733 ( 852) SS BOND : bond 0.00574 ( 7) SS BOND : angle 1.11080 ( 14) covalent geometry : bond 0.00419 ( 6489) covalent geometry : angle 0.54593 ( 8811) *********************** 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 86 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.721 Fit side-chains REVERT: A 108 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.8183 (mmm160) REVERT: A 253 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8067 (pt0) REVERT: B 19 LYS cc_start: 0.8775 (mmtt) cc_final: 0.7998 (mtpp) REVERT: B 38 ASP cc_start: 0.8627 (m-30) cc_final: 0.8382 (m-30) REVERT: D 159 ASN cc_start: 0.8834 (p0) cc_final: 0.8515 (p0) REVERT: D 190 HIS cc_start: 0.8863 (m90) cc_final: 0.8491 (m90) REVERT: D 212 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7730 (ttp-170) outliers start: 7 outliers final: 6 residues processed: 83 average time/residue: 0.2680 time to fit residues: 27.5725 Evaluate side-chains 84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET 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 203 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.111008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.071496 restraints weight = 9378.506| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.92 r_work: 0.2638 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6496 Z= 0.114 Angle : 0.508 11.558 8825 Z= 0.262 Chirality : 0.042 0.147 949 Planarity : 0.004 0.049 1138 Dihedral : 4.116 18.614 881 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.01 % Allowed : 9.35 % 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: 0.77 (0.30), residues: 788 helix: 1.02 (0.53), residues: 98 sheet: 1.49 (0.29), residues: 341 loop : -0.66 (0.31), residues: 349 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 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 278) hydrogen bonds : angle 4.77655 ( 852) SS BOND : bond 0.00483 ( 7) SS BOND : angle 0.88835 ( 14) covalent geometry : bond 0.00266 ( 6489) covalent geometry : angle 0.50751 ( 8811) *********************** 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: 7 poor density : 78 time to evaluate : 0.768 Fit side-chains REVERT: A 108 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8139 (mmm160) REVERT: A 173 GLU cc_start: 0.8751 (tp30) cc_final: 0.8127 (mt-10) REVERT: B 19 LYS cc_start: 0.8735 (mmtt) cc_final: 0.7964 (mtpp) REVERT: B 38 ASP cc_start: 0.8562 (m-30) cc_final: 0.8316 (m-30) REVERT: D 159 ASN cc_start: 0.8849 (p0) cc_final: 0.8534 (p0) REVERT: D 190 HIS cc_start: 0.8831 (m90) cc_final: 0.8423 (m90) outliers start: 7 outliers final: 5 residues processed: 83 average time/residue: 0.2793 time to fit residues: 29.1584 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 : 0.751 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 7 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 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 17 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 = 0.3371 r_free = 0.3371 target = 0.106825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.067805 restraints weight = 9234.255| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.88 r_work: 0.2613 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 6496 Z= 0.164 Angle : 0.534 11.845 8825 Z= 0.274 Chirality : 0.044 0.150 949 Planarity : 0.004 0.047 1138 Dihedral : 4.206 19.985 881 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.72 % Allowed : 10.07 % 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: 0.83 (0.30), residues: 788 helix: 0.95 (0.52), residues: 98 sheet: 1.55 (0.29), residues: 339 loop : -0.59 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.003 0.001 HIS C 5 PHE 0.011 0.001 PHE D 140 TYR 0.015 0.001 TYR E 33 ARG 0.005 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 278) hydrogen bonds : angle 4.81873 ( 852) SS BOND : bond 0.00522 ( 7) SS BOND : angle 1.10795 ( 14) covalent geometry : bond 0.00400 ( 6489) covalent geometry : angle 0.53272 ( 8811) *********************** 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 80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.732 Fit side-chains REVERT: A 108 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8179 (mmm160) REVERT: A 173 GLU cc_start: 0.8796 (tp30) cc_final: 0.8224 (mt-10) REVERT: A 253 GLN cc_start: 0.8096 (pt0) cc_final: 0.7326 (pm20) REVERT: B 19 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8050 (mtpp) REVERT: D 159 ASN cc_start: 0.8886 (p0) cc_final: 0.8545 (p0) REVERT: D 190 HIS cc_start: 0.8860 (m90) cc_final: 0.8423 (m90) REVERT: D 212 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7749 (ttp80) outliers start: 5 outliers final: 5 residues processed: 79 average time/residue: 0.2478 time to fit residues: 24.5092 Evaluate side-chains 78 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.109162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.069536 restraints weight = 9392.678| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.91 r_work: 0.2602 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6496 Z= 0.183 Angle : 0.553 12.128 8825 Z= 0.283 Chirality : 0.044 0.152 949 Planarity : 0.004 0.046 1138 Dihedral : 4.281 22.550 881 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.01 % Allowed : 10.07 % Favored : 88.92 % 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: 0.89 (0.52), residues: 98 sheet: 1.56 (0.28), residues: 343 loop : -0.53 (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 0.012 0.002 PHE D 140 TYR 0.015 0.001 TYR E 33 ARG 0.005 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 278) hydrogen bonds : angle 4.85125 ( 852) SS BOND : bond 0.00567 ( 7) SS BOND : angle 1.18081 ( 14) covalent geometry : bond 0.00448 ( 6489) covalent geometry : angle 0.55103 ( 8811) *********************** 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 79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.802 Fit side-chains REVERT: A 108 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.8090 (mmm160) REVERT: A 173 GLU cc_start: 0.8753 (tp30) cc_final: 0.8164 (mt-10) REVERT: A 253 GLN cc_start: 0.8268 (pt0) cc_final: 0.7587 (pm20) REVERT: B 19 LYS cc_start: 0.8775 (mmtt) cc_final: 0.7999 (mtpp) REVERT: E 199 TYR cc_start: 0.7474 (m-80) cc_final: 0.7129 (m-80) REVERT: D 159 ASN cc_start: 0.8866 (p0) cc_final: 0.8535 (p0) REVERT: D 190 HIS cc_start: 0.8848 (m90) cc_final: 0.8073 (m90) REVERT: D 212 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7785 (mtm180) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.2757 time to fit residues: 26.7801 Evaluate side-chains 76 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 33 LEU 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: 0.0060 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.111325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.071890 restraints weight = 9357.601| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.91 r_work: 0.2648 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6496 Z= 0.108 Angle : 0.495 11.106 8825 Z= 0.255 Chirality : 0.042 0.132 949 Planarity : 0.004 0.046 1138 Dihedral : 4.024 19.640 881 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.72 % Allowed : 10.94 % Favored : 88.35 % 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: 1.01 (0.30), residues: 788 helix: 1.12 (0.53), residues: 98 sheet: 1.62 (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 A 244 HIS 0.002 0.000 HIS B 51 PHE 0.008 0.001 PHE A 33 TYR 0.013 0.001 TYR E 33 ARG 0.002 0.000 ARG D 212 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 278) hydrogen bonds : angle 4.57301 ( 852) SS BOND : bond 0.00444 ( 7) SS BOND : angle 0.90663 ( 14) covalent geometry : bond 0.00252 ( 6489) covalent geometry : angle 0.49390 ( 8811) *********************** 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 78 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.743 Fit side-chains REVERT: A 108 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.8158 (mmm160) REVERT: A 173 GLU cc_start: 0.8773 (tp30) cc_final: 0.8192 (mt-10) REVERT: A 253 GLN cc_start: 0.8381 (pt0) cc_final: 0.7722 (pm20) REVERT: B 19 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8027 (mtpp) REVERT: E 199 TYR cc_start: 0.7410 (m-80) cc_final: 0.7098 (m-80) REVERT: D 159 ASN cc_start: 0.8862 (p0) cc_final: 0.8532 (p0) REVERT: D 190 HIS cc_start: 0.8821 (m90) cc_final: 0.8190 (m90) REVERT: D 212 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7709 (mtm180) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.2619 time to fit residues: 25.1782 Evaluate side-chains 76 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP 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: 1.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.110270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.070666 restraints weight = 9486.868| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.93 r_work: 0.2624 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6496 Z= 0.146 Angle : 0.528 11.647 8825 Z= 0.270 Chirality : 0.043 0.143 949 Planarity : 0.004 0.045 1138 Dihedral : 4.087 20.039 881 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.72 % Allowed : 11.37 % Favored : 87.91 % 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: 1.11 (0.52), residues: 98 sheet: 1.62 (0.28), residues: 344 loop : -0.42 (0.32), residues: 346 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 0.015 0.001 TYR E 33 ARG 0.004 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 278) hydrogen bonds : angle 4.62454 ( 852) SS BOND : bond 0.00506 ( 7) SS BOND : angle 1.05758 ( 14) covalent geometry : bond 0.00353 ( 6489) covalent geometry : angle 0.52637 ( 8811) *********************** 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 78 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.684 Fit side-chains REVERT: A 108 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.8139 (mmm160) REVERT: A 173 GLU cc_start: 0.8766 (tp30) cc_final: 0.8167 (mt-10) REVERT: A 253 GLN cc_start: 0.8371 (pt0) cc_final: 0.7756 (pm20) REVERT: B 19 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8045 (mtpp) REVERT: E 199 TYR cc_start: 0.7426 (m-80) cc_final: 0.7126 (m-80) REVERT: D 159 ASN cc_start: 0.8895 (p0) cc_final: 0.8560 (p0) REVERT: D 190 HIS cc_start: 0.8881 (m90) cc_final: 0.8081 (m90) REVERT: D 212 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7828 (mtm180) outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 0.2508 time to fit residues: 24.1898 Evaluate side-chains 78 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 73 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.111615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.072109 restraints weight = 9431.862| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.93 r_work: 0.2655 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6496 Z= 0.108 Angle : 0.499 10.979 8825 Z= 0.256 Chirality : 0.042 0.132 949 Planarity : 0.004 0.045 1138 Dihedral : 3.942 17.681 881 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.58 % Allowed : 11.51 % Favored : 87.91 % 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: 1.15 (0.53), residues: 98 sheet: 1.63 (0.29), residues: 343 loop : -0.28 (0.32), residues: 347 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 0.008 0.001 PHE A 33 TYR 0.013 0.001 TYR E 33 ARG 0.002 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 278) hydrogen bonds : angle 4.47984 ( 852) SS BOND : bond 0.00459 ( 7) SS BOND : angle 0.90078 ( 14) covalent geometry : bond 0.00252 ( 6489) covalent geometry : angle 0.49828 ( 8811) ********************** 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 79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.748 Fit side-chains REVERT: A 108 ARG cc_start: 0.8371 (mmm-85) cc_final: 0.8142 (mmm160) REVERT: A 173 GLU cc_start: 0.8746 (tp30) cc_final: 0.8144 (mt-10) REVERT: A 253 GLN cc_start: 0.8457 (pt0) cc_final: 0.7710 (pm20) REVERT: B 19 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8024 (mtpp) REVERT: E 199 TYR cc_start: 0.7342 (m-80) cc_final: 0.7035 (m-80) REVERT: E 211 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8433 (mmmm) REVERT: D 159 ASN cc_start: 0.8897 (p0) cc_final: 0.8534 (p0) REVERT: D 190 HIS cc_start: 0.8859 (m90) cc_final: 0.8416 (m90) outliers start: 4 outliers final: 3 residues processed: 78 average time/residue: 0.2551 time to fit residues: 25.0656 Evaluate side-chains 77 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.110973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.071329 restraints weight = 9546.412| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.95 r_work: 0.2636 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6496 Z= 0.129 Angle : 0.517 11.457 8825 Z= 0.264 Chirality : 0.042 0.141 949 Planarity : 0.004 0.045 1138 Dihedral : 3.992 17.510 881 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.72 % Allowed : 11.22 % Favored : 88.06 % 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: 1.12 (0.30), residues: 788 helix: 1.14 (0.53), residues: 98 sheet: 1.63 (0.29), residues: 343 loop : -0.28 (0.32), residues: 347 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 6 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 278) hydrogen bonds : angle 4.51412 ( 852) SS BOND : bond 0.00472 ( 7) SS BOND : angle 0.97377 ( 14) covalent geometry : bond 0.00310 ( 6489) covalent geometry : angle 0.51583 ( 8811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6375.22 seconds wall clock time: 113 minutes 37.55 seconds (6817.55 seconds total)