Starting phenix.real_space_refine on Fri Dec 27 10:31:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tc3_41151/12_2024/8tc3_41151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tc3_41151/12_2024/8tc3_41151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tc3_41151/12_2024/8tc3_41151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tc3_41151/12_2024/8tc3_41151.map" model { file = "/net/cci-nas-00/data/ceres_data/8tc3_41151/12_2024/8tc3_41151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tc3_41151/12_2024/8tc3_41151.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 46 5.16 5 C 2570 2.51 5 N 700 2.21 5 O 809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4129 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2052 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "B" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2052 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 684 SG CYS A 97 19.145 34.501 42.446 1.00 16.69 S ATOM 939 SG CYS A 132 24.431 37.443 41.514 1.00 12.41 S ATOM 2736 SG CYS B 97 19.867 37.778 36.754 1.00 19.30 S ATOM 2991 SG CYS B 132 23.288 32.561 37.759 1.00 17.13 S Time building chain proxies: 5.37, per 1000 atoms: 1.30 Number of scatterers: 4129 At special positions: 0 Unit cell: (65.65, 65.65, 80.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 46 16.00 O 809 8.00 N 700 7.00 C 2570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.16 Conformation dependent library (CDL) restraints added in 571.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS A 97 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS A 132 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 132 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 97 " Number of angles added : 12 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 53.7% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 97 through 113 removed outlier: 3.592A pdb=" N GLY A 101 " --> pdb=" O CYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 154 through 172 Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 214 through 223 removed outlier: 4.067A pdb=" N GLN A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 234 through 249 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'B' and resid 14 through 29 Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.820A pdb=" N GLY B 101 " --> pdb=" O CYS B 97 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 154 through 173 removed outlier: 3.794A pdb=" N ASN B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 214 through 223 removed outlier: 4.024A pdb=" N GLN B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 234 through 249 Processing helix chain 'B' and resid 260 through 271 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 removed outlier: 6.521A pdb=" N MET A 34 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASP A 125 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 36 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN A 4 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N TYR A 148 " --> pdb=" O GLN A 4 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA A 6 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A 150 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR A 8 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 147 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE A 183 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 149 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN A 185 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N CYS A 151 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N MET A 207 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N GLY A 180 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS A 209 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 182 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A 211 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS A 184 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 78 removed outlier: 6.623A pdb=" N GLN B 4 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TYR B 148 " --> pdb=" O GLN B 4 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA B 6 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 150 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR B 8 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 147 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE B 183 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE B 149 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B 185 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N CYS B 151 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 12.922A pdb=" N MET B 207 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 10.653A pdb=" N GLY B 180 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N HIS B 209 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 182 " --> pdb=" O HIS B 209 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL B 211 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS B 184 " --> pdb=" O VAL B 211 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.44: 1649 1.44 - 1.65: 2431 1.65 - 1.86: 70 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 4162 Sorted by residual: bond pdb=" C ILE B 273 " pdb=" O ILE B 273 " ideal model delta sigma weight residual 1.231 1.241 -0.009 1.02e-02 9.61e+03 8.34e-01 bond pdb=" C TYR A 8 " pdb=" N GLY A 9 " ideal model delta sigma weight residual 1.319 1.328 -0.009 1.34e-02 5.57e+03 4.78e-01 bond pdb=" C MET A 137 " pdb=" O MET A 137 " ideal model delta sigma weight residual 1.244 1.237 0.007 1.00e-02 1.00e+04 4.25e-01 bond pdb=" CA GLY A 96 " pdb=" C GLY A 96 " ideal model delta sigma weight residual 1.523 1.514 0.009 1.36e-02 5.41e+03 4.18e-01 bond pdb=" CB MET B 155 " pdb=" CG MET B 155 " ideal model delta sigma weight residual 1.520 1.501 0.019 3.00e-02 1.11e+03 3.90e-01 ... (remaining 4157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 5515 1.48 - 2.96: 84 2.96 - 4.44: 6 4.44 - 5.92: 2 5.92 - 7.40: 1 Bond angle restraints: 5608 Sorted by residual: angle pdb=" NE ARG B 100 " pdb=" CZ ARG B 100 " pdb=" NH2 ARG B 100 " ideal model delta sigma weight residual 119.20 121.48 -2.28 9.00e-01 1.23e+00 6.44e+00 angle pdb=" NE ARG B 100 " pdb=" CZ ARG B 100 " pdb=" NH1 ARG B 100 " ideal model delta sigma weight residual 121.50 119.16 2.34 1.00e+00 1.00e+00 5.46e+00 angle pdb=" C CYS A 38 " pdb=" N ASP A 39 " pdb=" CA ASP A 39 " ideal model delta sigma weight residual 121.27 128.67 -7.40 3.40e+00 8.65e-02 4.74e+00 angle pdb=" C ALA A 136 " pdb=" N MET A 137 " pdb=" CA MET A 137 " ideal model delta sigma weight residual 120.26 122.64 -2.38 1.34e+00 5.57e-01 3.15e+00 angle pdb=" CA GLY B 9 " pdb=" C GLY B 9 " pdb=" N LYS B 10 " ideal model delta sigma weight residual 115.34 116.70 -1.36 8.10e-01 1.52e+00 2.81e+00 ... (remaining 5603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 2196 17.90 - 35.79: 251 35.79 - 53.69: 78 53.69 - 71.59: 16 71.59 - 89.48: 11 Dihedral angle restraints: 2552 sinusoidal: 1020 harmonic: 1532 Sorted by residual: dihedral pdb=" CA ASP A 39 " pdb=" CB ASP A 39 " pdb=" CG ASP A 39 " pdb=" OD1 ASP A 39 " ideal model delta sinusoidal sigma weight residual -30.00 -89.08 59.08 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP A 262 " pdb=" CB ASP A 262 " pdb=" CG ASP A 262 " pdb=" OD1 ASP A 262 " ideal model delta sinusoidal sigma weight residual -30.00 -87.79 57.79 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP B 262 " pdb=" CB ASP B 262 " pdb=" CG ASP B 262 " pdb=" OD1 ASP B 262 " ideal model delta sinusoidal sigma weight residual -30.00 -87.22 57.22 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 2549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 384 0.028 - 0.056: 161 0.056 - 0.084: 57 0.084 - 0.112: 31 0.112 - 0.140: 11 Chirality restraints: 644 Sorted by residual: chirality pdb=" CA ILE B 255 " pdb=" N ILE B 255 " pdb=" C ILE B 255 " pdb=" CB ILE B 255 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL B 150 " pdb=" N VAL B 150 " pdb=" C VAL B 150 " pdb=" CB VAL B 150 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 641 not shown) Planarity restraints: 730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 130 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C VAL A 130 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL A 130 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 131 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 211 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.70e-01 pdb=" N PRO B 212 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " 0.014 5.00e-02 4.00e+02 2.06e-02 6.76e-01 pdb=" N PRO A 212 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.011 5.00e-02 4.00e+02 ... (remaining 727 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 972 2.79 - 3.32: 3856 3.32 - 3.85: 7462 3.85 - 4.37: 9078 4.37 - 4.90: 14890 Nonbonded interactions: 36258 Sorted by model distance: nonbonded pdb=" O GLY A 133 " pdb=" NH2 ARG A 140 " model vdw 2.266 3.120 nonbonded pdb=" O GLY A 94 " pdb=" OH TYR B 171 " model vdw 2.289 3.040 nonbonded pdb=" NE2 GLN B 145 " pdb=" OG SER B 176 " model vdw 2.301 3.120 nonbonded pdb=" OG1 THR B 45 " pdb=" OE1 GLN B 54 " model vdw 2.301 3.040 nonbonded pdb=" NZ LYS B 10 " pdb=" O GLY B 11 " model vdw 2.337 3.120 ... (remaining 36253 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 274) } 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: 0.010 Normalize map: mean=0, sd=1: 4.860 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.820 Find NCS groups from input model: 0.160 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.003 0.020 4162 Z= 0.165 Angle : 0.475 7.399 5608 Z= 0.266 Chirality : 0.040 0.140 644 Planarity : 0.003 0.023 730 Dihedral : 18.012 89.482 1576 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.46 % Allowed : 25.00 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.36), residues: 534 helix: 1.69 (0.34), residues: 248 sheet: -0.80 (0.54), residues: 84 loop : -0.83 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.010 0.001 PHE A 271 TYR 0.009 0.001 TYR B 80 ARG 0.004 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.537 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 82 average time/residue: 1.4937 time to fit residues: 126.2534 Evaluate side-chains 81 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4162 Z= 0.176 Angle : 0.445 5.013 5608 Z= 0.241 Chirality : 0.042 0.152 644 Planarity : 0.003 0.025 730 Dihedral : 4.376 24.309 584 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 4.13 % Allowed : 21.33 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.37), residues: 534 helix: 1.96 (0.34), residues: 252 sheet: -0.91 (0.55), residues: 84 loop : -0.62 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.011 0.001 PHE B 271 TYR 0.008 0.001 TYR B 80 ARG 0.005 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.440 Fit side-chains REVERT: A 206 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: B 60 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.6840 (mtp) REVERT: B 73 GLU cc_start: 0.8183 (mp0) cc_final: 0.7391 (tm-30) REVERT: B 261 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7905 (mmm) outliers start: 18 outliers final: 4 residues processed: 96 average time/residue: 1.5400 time to fit residues: 152.1069 Evaluate side-chains 83 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 261 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4162 Z= 0.241 Angle : 0.471 5.114 5608 Z= 0.252 Chirality : 0.043 0.148 644 Planarity : 0.003 0.022 730 Dihedral : 4.565 26.480 584 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.90 % Allowed : 22.02 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.37), residues: 534 helix: 1.88 (0.34), residues: 250 sheet: -1.08 (0.54), residues: 86 loop : -0.63 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.012 0.002 PHE B 271 TYR 0.010 0.001 TYR B 80 ARG 0.003 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.527 Fit side-chains REVERT: A 155 MET cc_start: 0.8168 (tmm) cc_final: 0.7917 (tmt) REVERT: A 156 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7501 (mmp) REVERT: A 206 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8152 (pt0) REVERT: A 215 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.7229 (m-40) REVERT: B 60 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6833 (mtp) REVERT: B 73 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7397 (tm-30) outliers start: 17 outliers final: 4 residues processed: 89 average time/residue: 1.5247 time to fit residues: 139.6059 Evaluate side-chains 87 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 266 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4162 Z= 0.188 Angle : 0.440 5.052 5608 Z= 0.236 Chirality : 0.042 0.143 644 Planarity : 0.003 0.026 730 Dihedral : 4.421 25.241 584 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.67 % Allowed : 22.25 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.37), residues: 534 helix: 2.04 (0.34), residues: 250 sheet: -0.91 (0.56), residues: 78 loop : -0.61 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.012 0.002 PHE B 271 TYR 0.006 0.001 TYR B 80 ARG 0.005 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.454 Fit side-chains REVERT: A 206 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: B 60 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6792 (mtp) REVERT: B 73 GLU cc_start: 0.8131 (mp0) cc_final: 0.7401 (tm-30) outliers start: 16 outliers final: 5 residues processed: 89 average time/residue: 1.4789 time to fit residues: 135.6134 Evaluate side-chains 84 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 266 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4162 Z= 0.167 Angle : 0.428 5.012 5608 Z= 0.229 Chirality : 0.041 0.142 644 Planarity : 0.003 0.028 730 Dihedral : 4.307 23.661 584 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.29 % Allowed : 23.85 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.37), residues: 534 helix: 2.13 (0.34), residues: 250 sheet: -0.97 (0.56), residues: 78 loop : -0.60 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.012 0.001 PHE B 271 TYR 0.006 0.001 TYR A 171 ARG 0.006 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.533 Fit side-chains REVERT: A 141 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8383 (mm-30) REVERT: A 215 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7205 (m-40) REVERT: B 60 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.6771 (mtp) REVERT: B 73 GLU cc_start: 0.8111 (mp0) cc_final: 0.7383 (tm-30) outliers start: 10 outliers final: 3 residues processed: 89 average time/residue: 1.4935 time to fit residues: 136.8421 Evaluate side-chains 83 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 266 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4162 Z= 0.201 Angle : 0.447 5.049 5608 Z= 0.238 Chirality : 0.042 0.143 644 Planarity : 0.003 0.034 730 Dihedral : 4.365 23.996 583 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.98 % Allowed : 23.17 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.37), residues: 534 helix: 2.06 (0.34), residues: 250 sheet: -0.96 (0.55), residues: 78 loop : -0.58 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.013 0.002 PHE B 271 TYR 0.006 0.001 TYR B 80 ARG 0.006 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.495 Fit side-chains REVERT: A 29 MET cc_start: 0.7713 (mtp) cc_final: 0.7391 (mtp) REVERT: A 206 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: A 215 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.7226 (m-40) REVERT: A 235 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7731 (mttm) REVERT: B 60 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.6803 (mtp) REVERT: B 73 GLU cc_start: 0.8127 (mp0) cc_final: 0.7396 (tm-30) outliers start: 13 outliers final: 4 residues processed: 84 average time/residue: 1.4775 time to fit residues: 127.9449 Evaluate side-chains 84 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 266 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4162 Z= 0.235 Angle : 0.469 5.078 5608 Z= 0.248 Chirality : 0.042 0.144 644 Planarity : 0.003 0.033 730 Dihedral : 4.515 25.566 583 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.21 % Allowed : 22.48 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.37), residues: 534 helix: 1.99 (0.34), residues: 250 sheet: -0.97 (0.55), residues: 78 loop : -0.59 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.013 0.002 PHE B 271 TYR 0.007 0.001 TYR B 80 ARG 0.006 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.516 Fit side-chains REVERT: A 155 MET cc_start: 0.8200 (tmm) cc_final: 0.7923 (tmt) REVERT: A 156 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7111 (mmm) REVERT: A 206 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: A 215 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7238 (m-40) REVERT: A 235 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7724 (mttm) REVERT: A 274 MET cc_start: 0.7274 (ppp) cc_final: 0.6920 (ppp) REVERT: B 60 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6857 (mtp) REVERT: B 73 GLU cc_start: 0.8158 (mp0) cc_final: 0.7421 (tm-30) outliers start: 14 outliers final: 4 residues processed: 86 average time/residue: 1.4646 time to fit residues: 129.7113 Evaluate side-chains 85 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 266 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 45 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4162 Z= 0.173 Angle : 0.440 5.007 5608 Z= 0.235 Chirality : 0.041 0.142 644 Planarity : 0.003 0.042 730 Dihedral : 4.332 23.904 583 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.29 % Allowed : 23.62 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.37), residues: 534 helix: 2.14 (0.34), residues: 250 sheet: -1.01 (0.56), residues: 78 loop : -0.57 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.012 0.001 PHE B 271 TYR 0.005 0.001 TYR A 171 ARG 0.007 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.502 Fit side-chains REVERT: A 206 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: A 215 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7205 (m-40) REVERT: A 274 MET cc_start: 0.7211 (ppp) cc_final: 0.6817 (ppp) REVERT: B 60 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6755 (mtp) REVERT: B 71 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7398 (mm-30) REVERT: B 73 GLU cc_start: 0.8139 (mp0) cc_final: 0.7427 (tm-30) outliers start: 10 outliers final: 4 residues processed: 85 average time/residue: 1.5036 time to fit residues: 131.5767 Evaluate side-chains 84 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 266 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.0030 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4162 Z= 0.161 Angle : 0.431 4.999 5608 Z= 0.230 Chirality : 0.041 0.145 644 Planarity : 0.003 0.042 730 Dihedral : 4.257 22.567 583 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.61 % Allowed : 24.31 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.37), residues: 534 helix: 2.15 (0.34), residues: 252 sheet: -1.02 (0.56), residues: 78 loop : -0.50 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.012 0.002 PHE B 271 TYR 0.005 0.001 TYR A 171 ARG 0.008 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.459 Fit side-chains REVERT: A 206 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: A 215 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7195 (m-40) REVERT: A 235 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7715 (mttm) REVERT: B 60 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6748 (mtp) REVERT: B 71 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7411 (mm-30) REVERT: B 73 GLU cc_start: 0.8130 (mp0) cc_final: 0.7430 (tm-30) REVERT: B 100 ARG cc_start: 0.7855 (mtm110) cc_final: 0.6931 (mmp80) outliers start: 7 outliers final: 3 residues processed: 82 average time/residue: 1.4933 time to fit residues: 126.1081 Evaluate side-chains 83 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 266 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4162 Z= 0.263 Angle : 0.499 5.173 5608 Z= 0.263 Chirality : 0.043 0.145 644 Planarity : 0.003 0.041 730 Dihedral : 4.482 18.394 582 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.61 % Allowed : 24.54 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.37), residues: 534 helix: 1.90 (0.34), residues: 250 sheet: -0.98 (0.55), residues: 78 loop : -0.56 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.013 0.002 PHE B 271 TYR 0.008 0.002 TYR B 80 ARG 0.011 0.001 ARG A 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.443 Fit side-chains REVERT: A 155 MET cc_start: 0.8201 (tmm) cc_final: 0.7921 (tmt) REVERT: A 206 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: A 215 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7254 (m-40) REVERT: A 235 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7729 (mttm) REVERT: B 60 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.6868 (mtp) REVERT: B 71 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7411 (mm-30) REVERT: B 73 GLU cc_start: 0.8159 (mp0) cc_final: 0.7426 (tm-30) REVERT: B 100 ARG cc_start: 0.7854 (mtm110) cc_final: 0.6959 (mmp80) outliers start: 7 outliers final: 3 residues processed: 83 average time/residue: 1.4974 time to fit residues: 127.8876 Evaluate side-chains 83 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 266 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.137252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117292 restraints weight = 3861.802| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.57 r_work: 0.3182 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4162 Z= 0.203 Angle : 0.472 5.047 5608 Z= 0.249 Chirality : 0.042 0.142 644 Planarity : 0.003 0.039 730 Dihedral : 4.362 20.793 582 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.06 % Allowed : 24.31 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.37), residues: 534 helix: 1.99 (0.34), residues: 250 sheet: -1.00 (0.56), residues: 78 loop : -0.54 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.013 0.002 PHE B 271 TYR 0.006 0.001 TYR B 80 ARG 0.010 0.000 ARG A 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2583.12 seconds wall clock time: 47 minutes 11.35 seconds (2831.35 seconds total)