Starting phenix.real_space_refine on Fri Aug 22 17:13:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fjb_29221/08_2025/8fjb_29221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fjb_29221/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fjb_29221/08_2025/8fjb_29221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fjb_29221/08_2025/8fjb_29221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fjb_29221/08_2025/8fjb_29221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fjb_29221/08_2025/8fjb_29221.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.66, per 1000 atoms: 0.26 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: 0.50 Conformation dependent library (CDL) restraints added in 354.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.28 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: 0.78 Time building geometry restraints manager: 0.66 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: 3.860 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.28), 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 ARG 0.008 0.001 ARG A 6 TYR 0.024 0.002 TYR E 33 PHE 0.029 0.002 PHE B 70 TRP 0.016 0.001 TRP A 244 HIS 0.005 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 6489) covalent geometry : angle 0.68320 ( 8811) SS BOND : bond 0.00562 ( 7) SS BOND : angle 1.39339 ( 14) hydrogen bonds : bond 0.23165 ( 278) hydrogen bonds : angle 8.99180 ( 852) *********************** 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 : 0.182 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: 0.1235 time to fit residues: 13.1773 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 : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.110106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.070103 restraints weight = 9428.540| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.96 r_work: 0.2592 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6496 Z= 0.187 Angle : 0.594 11.791 8825 Z= 0.308 Chirality : 0.046 0.232 949 Planarity : 0.005 0.053 1138 Dihedral : 4.544 18.126 881 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.43 % Allowed : 5.04 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.29), residues: 788 helix: 0.12 (0.51), residues: 98 sheet: 0.55 (0.27), residues: 362 loop : -1.30 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 6 TYR 0.018 0.002 TYR E 33 PHE 0.016 0.002 PHE B 70 TRP 0.013 0.001 TRP A 244 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 6489) covalent geometry : angle 0.59198 ( 8811) SS BOND : bond 0.00666 ( 7) SS BOND : angle 1.24404 ( 14) hydrogen bonds : bond 0.05012 ( 278) hydrogen bonds : angle 5.80584 ( 852) *********************** 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 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.259 Fit side-chains REVERT: A 108 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.8093 (mmm160) REVERT: A 113 TYR cc_start: 0.8476 (m-80) cc_final: 0.8266 (m-80) REVERT: B 19 LYS cc_start: 0.8763 (mmtt) cc_final: 0.7988 (mtpp) REVERT: B 34 ASP cc_start: 0.8886 (m-30) cc_final: 0.8664 (m-30) REVERT: B 38 ASP cc_start: 0.8632 (m-30) cc_final: 0.8367 (m-30) REVERT: D 159 ASN cc_start: 0.8847 (p0) cc_final: 0.8460 (p0) REVERT: D 190 HIS cc_start: 0.8804 (m90) cc_final: 0.8507 (m90) outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.1162 time to fit residues: 12.8598 Evaluate side-chains 86 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.109176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.069722 restraints weight = 9366.336| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.90 r_work: 0.2605 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6496 Z= 0.166 Angle : 0.552 12.038 8825 Z= 0.285 Chirality : 0.044 0.188 949 Planarity : 0.004 0.050 1138 Dihedral : 4.361 19.602 881 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.86 % Allowed : 6.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.30), residues: 788 helix: 0.62 (0.52), residues: 98 sheet: 1.05 (0.28), residues: 347 loop : -1.00 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 6 TYR 0.017 0.001 TYR E 33 PHE 0.013 0.002 PHE B 70 TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6489) covalent geometry : angle 0.55071 ( 8811) SS BOND : bond 0.00599 ( 7) SS BOND : angle 1.12616 ( 14) hydrogen bonds : bond 0.04559 ( 278) hydrogen bonds : angle 5.26878 ( 852) *********************** 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 87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.346 Fit side-chains REVERT: A 89 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8301 (mp0) REVERT: A 113 TYR cc_start: 0.8473 (m-80) cc_final: 0.7999 (m-80) REVERT: A 173 GLU cc_start: 0.8748 (tp30) cc_final: 0.8172 (mt-10) REVERT: B 19 LYS cc_start: 0.8786 (mmtt) cc_final: 0.7981 (mtpp) REVERT: B 34 ASP cc_start: 0.8852 (m-30) cc_final: 0.8641 (m-30) REVERT: B 38 ASP cc_start: 0.8603 (m-30) cc_final: 0.8352 (m-30) REVERT: D 159 ASN cc_start: 0.8795 (p0) cc_final: 0.8495 (p0) REVERT: D 188 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8629 (mm-30) REVERT: D 190 HIS cc_start: 0.8879 (m90) cc_final: 0.8418 (m90) outliers start: 6 outliers final: 6 residues processed: 85 average time/residue: 0.1129 time to fit residues: 11.9215 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 : 0.260 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 153 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 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 = 0.3411 r_free = 0.3411 target = 0.110260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.070780 restraints weight = 9378.316| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.90 r_work: 0.2626 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6496 Z= 0.134 Angle : 0.515 11.471 8825 Z= 0.266 Chirality : 0.043 0.159 949 Planarity : 0.004 0.050 1138 Dihedral : 4.177 19.110 881 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.86 % Allowed : 8.35 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.30), residues: 788 helix: 0.93 (0.53), residues: 98 sheet: 1.30 (0.28), residues: 341 loop : -0.78 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 108 TYR 0.015 0.001 TYR E 33 PHE 0.011 0.001 PHE A 33 TRP 0.010 0.001 TRP A 244 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6489) covalent geometry : angle 0.51454 ( 8811) SS BOND : bond 0.00512 ( 7) SS BOND : angle 0.93948 ( 14) hydrogen bonds : bond 0.04030 ( 278) hydrogen bonds : angle 4.92666 ( 852) *********************** 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 87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.273 Fit side-chains REVERT: A 89 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8293 (mp0) REVERT: A 113 TYR cc_start: 0.8459 (m-80) cc_final: 0.7910 (m-80) REVERT: A 173 GLU cc_start: 0.8772 (tp30) cc_final: 0.8183 (mt-10) REVERT: B 19 LYS cc_start: 0.8755 (mmtt) cc_final: 0.7978 (mtpp) REVERT: B 34 ASP cc_start: 0.8839 (m-30) cc_final: 0.8619 (m-30) REVERT: B 38 ASP cc_start: 0.8573 (m-30) cc_final: 0.8328 (m-30) REVERT: D 159 ASN cc_start: 0.8817 (p0) cc_final: 0.8498 (p0) REVERT: D 190 HIS cc_start: 0.8886 (m90) cc_final: 0.8548 (m90) REVERT: D 212 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7745 (ttp80) outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.1106 time to fit residues: 11.7255 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 : 0.242 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 153 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.110458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.070848 restraints weight = 9555.819| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.94 r_work: 0.2624 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6496 Z= 0.134 Angle : 0.516 11.320 8825 Z= 0.266 Chirality : 0.043 0.148 949 Planarity : 0.004 0.048 1138 Dihedral : 4.123 18.831 881 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.30), residues: 788 helix: 1.04 (0.53), residues: 98 sheet: 1.46 (0.29), residues: 339 loop : -0.63 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 6 TYR 0.014 0.001 TYR E 33 PHE 0.010 0.001 PHE A 33 TRP 0.011 0.001 TRP A 244 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6489) covalent geometry : angle 0.51473 ( 8811) SS BOND : bond 0.00489 ( 7) SS BOND : angle 0.96323 ( 14) hydrogen bonds : bond 0.03992 ( 278) hydrogen bonds : angle 4.80645 ( 852) *********************** 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 81 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.201 Fit side-chains REVERT: A 108 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.8111 (mmm160) REVERT: A 113 TYR cc_start: 0.8472 (m-80) cc_final: 0.7884 (m-80) REVERT: A 173 GLU cc_start: 0.8796 (tp30) cc_final: 0.8208 (mt-10) REVERT: B 19 LYS cc_start: 0.8758 (mmtt) cc_final: 0.7980 (mtpp) REVERT: B 34 ASP cc_start: 0.8889 (m-30) cc_final: 0.8686 (m-30) REVERT: D 159 ASN cc_start: 0.8854 (p0) cc_final: 0.8525 (p0) REVERT: D 190 HIS cc_start: 0.8882 (m90) cc_final: 0.8409 (m90) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.1091 time to fit residues: 10.8610 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 : 0.214 ------------------------------------------------------------------------------- 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 153 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.109789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.072023 restraints weight = 9551.311| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.70 r_work: 0.2646 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 6496 Z= 0.236 Angle : 0.580 12.243 8825 Z= 0.298 Chirality : 0.045 0.167 949 Planarity : 0.004 0.047 1138 Dihedral : 4.418 23.506 881 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.29 % Allowed : 9.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.30), residues: 788 helix: 0.83 (0.52), residues: 98 sheet: 1.47 (0.28), residues: 343 loop : -0.59 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 6 TYR 0.017 0.002 TYR E 33 PHE 0.015 0.002 PHE D 140 TRP 0.012 0.001 TRP E 47 HIS 0.004 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 6489) covalent geometry : angle 0.57767 ( 8811) SS BOND : bond 0.00623 ( 7) SS BOND : angle 1.35098 ( 14) hydrogen bonds : bond 0.04960 ( 278) hydrogen bonds : angle 5.03868 ( 852) *********************** 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 87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.219 Fit side-chains REVERT: A 108 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.8171 (mmm160) REVERT: A 113 TYR cc_start: 0.8618 (m-80) cc_final: 0.8050 (m-80) REVERT: B 19 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8144 (mtpp) REVERT: B 34 ASP cc_start: 0.8886 (m-30) cc_final: 0.8676 (m-30) REVERT: D 159 ASN cc_start: 0.8980 (p0) cc_final: 0.8662 (p0) outliers start: 9 outliers final: 8 residues processed: 85 average time/residue: 0.1081 time to fit residues: 11.3672 Evaluate side-chains 84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 153 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 50 optimal weight: 0.3980 chunk 27 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.114054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.074351 restraints weight = 9600.351| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.84 r_work: 0.2712 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6496 Z= 0.105 Angle : 0.493 10.767 8825 Z= 0.254 Chirality : 0.042 0.141 949 Planarity : 0.004 0.047 1138 Dihedral : 4.035 19.816 881 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.86 % Allowed : 9.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.30), residues: 788 helix: 1.14 (0.53), residues: 98 sheet: 1.58 (0.29), residues: 337 loop : -0.47 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 212 TYR 0.013 0.001 TYR E 33 PHE 0.008 0.001 PHE A 8 TRP 0.009 0.001 TRP A 167 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6489) covalent geometry : angle 0.49212 ( 8811) SS BOND : bond 0.00471 ( 7) SS BOND : angle 0.86592 ( 14) hydrogen bonds : bond 0.03533 ( 278) hydrogen bonds : angle 4.62973 ( 852) *********************** 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: 6 poor density : 76 time to evaluate : 0.183 Fit side-chains REVERT: A 108 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8215 (mmm160) REVERT: A 113 TYR cc_start: 0.8440 (m-80) cc_final: 0.7868 (m-80) REVERT: A 173 GLU cc_start: 0.8797 (tp30) cc_final: 0.8258 (mt-10) REVERT: A 253 GLN cc_start: 0.8350 (mt0) cc_final: 0.8125 (pt0) REVERT: B 19 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8096 (mtpp) REVERT: B 34 ASP cc_start: 0.8929 (m-30) cc_final: 0.8724 (m-30) REVERT: E 199 TYR cc_start: 0.7460 (m-80) cc_final: 0.7127 (m-80) REVERT: D 24 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7627 (ttm-80) REVERT: D 159 ASN cc_start: 0.8899 (p0) cc_final: 0.8554 (p0) REVERT: D 190 HIS cc_start: 0.8970 (m90) cc_final: 0.8744 (m-70) outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.1018 time to fit residues: 10.2625 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 : 0.163 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 153 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 0.0970 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 overall best weight: 0.6136 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.109524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.070623 restraints weight = 9378.409| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.86 r_work: 0.2692 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2007 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= 0.116 Angle : 0.504 10.953 8825 Z= 0.258 Chirality : 0.042 0.137 949 Planarity : 0.004 0.046 1138 Dihedral : 3.974 18.427 881 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.30), residues: 788 helix: 1.13 (0.52), residues: 98 sheet: 1.59 (0.29), residues: 344 loop : -0.35 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 212 TYR 0.014 0.001 TYR E 33 PHE 0.009 0.001 PHE A 33 TRP 0.010 0.001 TRP A 244 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6489) covalent geometry : angle 0.50305 ( 8811) SS BOND : bond 0.00415 ( 7) SS BOND : angle 0.91269 ( 14) hydrogen bonds : bond 0.03719 ( 278) hydrogen bonds : angle 4.56557 ( 852) *********************** 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 80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 108 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8204 (mmm160) REVERT: A 113 TYR cc_start: 0.8486 (m-80) cc_final: 0.7908 (m-80) REVERT: A 173 GLU cc_start: 0.8817 (tp30) cc_final: 0.8307 (mt-10) REVERT: A 253 GLN cc_start: 0.8397 (mt0) cc_final: 0.8170 (pt0) REVERT: B 19 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8139 (mtpp) REVERT: E 199 TYR cc_start: 0.7439 (m-80) cc_final: 0.7142 (m-80) REVERT: D 159 ASN cc_start: 0.8967 (p0) cc_final: 0.8622 (p0) REVERT: D 190 HIS cc_start: 0.9002 (m90) cc_final: 0.8795 (m-70) outliers start: 5 outliers final: 3 residues processed: 79 average time/residue: 0.1168 time to fit residues: 11.4791 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 : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 153 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 64 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.107815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.068478 restraints weight = 9510.208| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.92 r_work: 0.2653 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6496 Z= 0.179 Angle : 0.552 12.160 8825 Z= 0.282 Chirality : 0.044 0.155 949 Planarity : 0.004 0.045 1138 Dihedral : 4.203 20.733 881 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.58 % Allowed : 11.22 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.30), residues: 788 helix: 1.04 (0.52), residues: 98 sheet: 1.53 (0.28), residues: 343 loop : -0.37 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 6 TYR 0.016 0.001 TYR E 33 PHE 0.011 0.002 PHE D 140 TRP 0.011 0.001 TRP A 244 HIS 0.003 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 6489) covalent geometry : angle 0.55027 ( 8811) SS BOND : bond 0.00544 ( 7) SS BOND : angle 1.18195 ( 14) hydrogen bonds : bond 0.04418 ( 278) hydrogen bonds : angle 4.76387 ( 852) *********************** 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: 4 poor density : 74 time to evaluate : 0.258 Fit side-chains REVERT: A 108 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8197 (mmm160) REVERT: A 113 TYR cc_start: 0.8582 (m-80) cc_final: 0.7964 (m-80) REVERT: A 173 GLU cc_start: 0.8814 (tp30) cc_final: 0.8283 (mt-10) REVERT: A 253 GLN cc_start: 0.8441 (mt0) cc_final: 0.8098 (pt0) REVERT: A 256 ARG cc_start: 0.8351 (mtp180) cc_final: 0.8035 (mtp-110) REVERT: B 19 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8085 (mtpp) REVERT: E 211 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8516 (mmmm) REVERT: D 159 ASN cc_start: 0.8987 (p0) cc_final: 0.8639 (p0) REVERT: D 190 HIS cc_start: 0.9059 (m90) cc_final: 0.8730 (m-70) outliers start: 4 outliers final: 4 residues processed: 77 average time/residue: 0.1244 time to fit residues: 11.7751 Evaluate side-chains 77 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 153 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.112723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.073248 restraints weight = 9550.783| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.81 r_work: 0.2695 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6496 Z= 0.127 Angle : 0.515 11.629 8825 Z= 0.263 Chirality : 0.042 0.137 949 Planarity : 0.004 0.045 1138 Dihedral : 4.057 19.501 881 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.42 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.30), residues: 788 helix: 1.07 (0.53), residues: 98 sheet: 1.59 (0.29), residues: 343 loop : -0.30 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 212 TYR 0.014 0.001 TYR E 33 PHE 0.009 0.001 PHE A 33 TRP 0.010 0.001 TRP A 244 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6489) covalent geometry : angle 0.51360 ( 8811) SS BOND : bond 0.00472 ( 7) SS BOND : angle 0.97098 ( 14) hydrogen bonds : bond 0.03818 ( 278) hydrogen bonds : angle 4.60271 ( 852) ********************** 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: 5 poor density : 75 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 108 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.8239 (mmm160) REVERT: A 113 TYR cc_start: 0.8490 (m-80) cc_final: 0.7891 (m-80) REVERT: A 173 GLU cc_start: 0.8825 (tp30) cc_final: 0.8274 (mt-10) REVERT: A 253 GLN cc_start: 0.8445 (mt0) cc_final: 0.8109 (pt0) REVERT: A 256 ARG cc_start: 0.8350 (mtp180) cc_final: 0.8044 (mtp-110) REVERT: B 19 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8104 (mtpp) REVERT: E 211 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8513 (mmmm) REVERT: D 159 ASN cc_start: 0.8961 (p0) cc_final: 0.8620 (p0) REVERT: D 190 HIS cc_start: 0.9015 (m90) cc_final: 0.8781 (m-70) outliers start: 5 outliers final: 5 residues processed: 79 average time/residue: 0.1244 time to fit residues: 12.0640 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 : 0.259 ------------------------------------------------------------------------------- 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 153 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.108707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.069105 restraints weight = 9440.372| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.94 r_work: 0.2659 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6496 Z= 0.159 Angle : 0.538 11.908 8825 Z= 0.275 Chirality : 0.043 0.146 949 Planarity : 0.004 0.045 1138 Dihedral : 4.131 20.363 881 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.30), residues: 788 helix: 1.06 (0.52), residues: 98 sheet: 1.57 (0.28), residues: 343 loop : -0.32 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 212 TYR 0.015 0.001 TYR E 33 PHE 0.010 0.001 PHE D 140 TRP 0.010 0.001 TRP A 244 HIS 0.003 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6489) covalent geometry : angle 0.53614 ( 8811) SS BOND : bond 0.00509 ( 7) SS BOND : angle 1.09762 ( 14) hydrogen bonds : bond 0.04179 ( 278) hydrogen bonds : angle 4.67583 ( 852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1896.46 seconds wall clock time: 33 minutes 5.83 seconds (1985.83 seconds total)