Starting phenix.real_space_refine on Wed Sep 17 05:41:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hs2_34983/09_2025/8hs2_34983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hs2_34983/09_2025/8hs2_34983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hs2_34983/09_2025/8hs2_34983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hs2_34983/09_2025/8hs2_34983.map" model { file = "/net/cci-nas-00/data/ceres_data/8hs2_34983/09_2025/8hs2_34983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hs2_34983/09_2025/8hs2_34983.cif" } resolution = 3.08 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= 0.012 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 34 5.16 5 C 3487 2.51 5 N 930 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5456 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1617 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Chain: "C" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1623 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "R" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2216 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 1.51, per 1000 atoms: 0.28 Number of scatterers: 5456 At special positions: 0 Unit cell: (69.888, 92.352, 138.112, 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 34 16.00 O 1005 8.00 N 930 7.00 C 3487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 374 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 480 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 122 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 171.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 13 sheets defined 39.1% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.753A pdb=" N TYR B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.666A pdb=" N SER B 110 " --> pdb=" O PRO B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.688A pdb=" N LEU C 411 " --> pdb=" O THR C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.538A pdb=" N HIS C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 49 removed outlier: 4.059A pdb=" N ALA R 39 " --> pdb=" O PHE R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 81 Processing helix chain 'R' and resid 86 through 116 Proline residue: R 107 - end of helix removed outlier: 4.233A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 122 No H-bonds generated for 'chain 'R' and resid 120 through 122' Processing helix chain 'R' and resid 123 through 151 removed outlier: 3.708A pdb=" N VAL R 127 " --> pdb=" O ALA R 123 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER R 137 " --> pdb=" O ASN R 133 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE R 138 " --> pdb=" O MET R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 187 removed outlier: 3.815A pdb=" N ALA R 167 " --> pdb=" O GLN R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 205 removed outlier: 3.913A pdb=" N VAL R 202 " --> pdb=" O PHE R 198 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU R 203 " --> pdb=" O ALA R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 225 Processing helix chain 'R' and resid 229 through 254 Processing helix chain 'R' and resid 254 through 267 removed outlier: 3.527A pdb=" N HIS R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA R 265 " --> pdb=" O GLN R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 293 removed outlier: 4.380A pdb=" N SER R 290 " --> pdb=" O SER R 286 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS R 291 " --> pdb=" O SER R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 301 removed outlier: 3.967A pdb=" N PHE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 317 removed outlier: 4.099A pdb=" N ALA R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.674A pdb=" N ILE B 53 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE B 69 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.161A pdb=" N TYR B 131 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA B 119 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE B 129 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 153 removed outlier: 4.015A pdb=" N GLY B 168 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 165 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 169 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 204 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 153 removed outlier: 4.015A pdb=" N GLY B 168 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 165 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 169 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 204 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 198 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AA7, first strand: chain 'C' and resid 292 through 293 removed outlier: 6.678A pdb=" N THR C 355 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AA9, first strand: chain 'C' and resid 319 through 321 Processing sheet with id=AB1, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AB2, first strand: chain 'C' and resid 371 through 372 Processing sheet with id=AB3, first strand: chain 'C' and resid 402 through 404 removed outlier: 3.742A pdb=" N VAL C 419 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR C 459 " --> pdb=" O ASN C 424 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 431 through 435 removed outlier: 4.009A pdb=" N LYS C 493 " --> pdb=" O CYS C 480 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 482 " --> pdb=" O VAL C 491 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 879 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: 0.79 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1723 1.34 - 1.46: 1339 1.46 - 1.58: 2481 1.58 - 1.70: 0 1.70 - 1.81: 44 Bond restraints: 5587 Sorted by residual: bond pdb=" CB GLN B 200 " pdb=" CG GLN B 200 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.77e+00 bond pdb=" CB LYS C 435 " pdb=" CG LYS C 435 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CA ASP R 269 " pdb=" CB ASP R 269 " ideal model delta sigma weight residual 1.529 1.555 -0.025 1.74e-02 3.30e+03 2.13e+00 bond pdb=" CB ASP B 108 " pdb=" CG ASP B 108 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" CB ASP R 269 " pdb=" CG ASP R 269 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.95e+00 ... (remaining 5582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 7437 2.23 - 4.46: 129 4.46 - 6.69: 40 6.69 - 8.92: 5 8.92 - 11.15: 2 Bond angle restraints: 7613 Sorted by residual: angle pdb=" CA GLN B 200 " pdb=" CB GLN B 200 " pdb=" CG GLN B 200 " ideal model delta sigma weight residual 114.10 124.52 -10.42 2.00e+00 2.50e-01 2.71e+01 angle pdb=" CA ARG C 442 " pdb=" CB ARG C 442 " pdb=" CG ARG C 442 " ideal model delta sigma weight residual 114.10 122.81 -8.71 2.00e+00 2.50e-01 1.90e+01 angle pdb=" CA LYS C 433 " pdb=" CB LYS C 433 " pdb=" CG LYS C 433 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CB LYS C 435 " pdb=" CG LYS C 435 " pdb=" CD LYS C 435 " ideal model delta sigma weight residual 111.30 119.88 -8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CA ASP R 269 " pdb=" CB ASP R 269 " pdb=" CG ASP R 269 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.00e+00 1.00e+00 1.38e+01 ... (remaining 7608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2921 17.85 - 35.70: 299 35.70 - 53.55: 71 53.55 - 71.40: 4 71.40 - 89.25: 7 Dihedral angle restraints: 3302 sinusoidal: 1237 harmonic: 2065 Sorted by residual: dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 122 " pdb=" CB CYS R 122 " ideal model delta sinusoidal sigma weight residual -86.00 -175.25 89.25 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CA LEU R 229 " pdb=" C LEU R 229 " pdb=" N HIS R 230 " pdb=" CA HIS R 230 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA SER C 402 " pdb=" C SER C 402 " pdb=" N ILE C 403 " pdb=" CA ILE C 403 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 3299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 665 0.044 - 0.088: 153 0.088 - 0.131: 61 0.131 - 0.175: 9 0.175 - 0.219: 4 Chirality restraints: 892 Sorted by residual: chirality pdb=" CA TYR C 426 " pdb=" N TYR C 426 " pdb=" C TYR C 426 " pdb=" CB TYR C 426 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL R 32 " pdb=" CA VAL R 32 " pdb=" CG1 VAL R 32 " pdb=" CG2 VAL R 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO C 427 " pdb=" N PRO C 427 " pdb=" C PRO C 427 " pdb=" CB PRO C 427 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 889 not shown) Planarity restraints: 954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 269 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ASP R 269 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP R 269 " 0.015 2.00e-02 2.50e+03 pdb=" N MET R 270 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 344 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO C 345 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 345 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 345 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 108 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" CG ASP B 108 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP B 108 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 108 " -0.012 2.00e-02 2.50e+03 ... (remaining 951 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 303 2.73 - 3.27: 5506 3.27 - 3.82: 9267 3.82 - 4.36: 10235 4.36 - 4.90: 18460 Nonbonded interactions: 43771 Sorted by model distance: nonbonded pdb=" O LEU C 392 " pdb=" OH TYR C 426 " model vdw 2.192 3.040 nonbonded pdb=" OG1 THR C 289 " pdb=" OE2 GLU C 379 " model vdw 2.249 3.040 nonbonded pdb=" OD2 ASP C 453 " pdb=" OG1 THR C 458 " model vdw 2.331 3.040 nonbonded pdb=" OG SER R 88 " pdb=" OD2 ASP R 147 " model vdw 2.333 3.040 nonbonded pdb=" N GLN R 305 " pdb=" OE1 GLN R 305 " model vdw 2.334 3.120 ... (remaining 43766 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: 1.410 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.650 Find NCS groups from input model: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.004 0.050 5592 Z= 0.177 Angle : 0.777 11.154 7623 Z= 0.410 Chirality : 0.046 0.219 892 Planarity : 0.005 0.054 954 Dihedral : 14.964 85.417 1963 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.17 % Allowed : 19.31 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.10 (0.31), residues: 708 helix: 1.52 (0.32), residues: 244 sheet: 0.12 (0.38), residues: 186 loop : -1.28 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 310 TYR 0.008 0.001 TYR B 66 PHE 0.014 0.001 PHE B 69 TRP 0.007 0.001 TRP B 183 HIS 0.005 0.001 HIS C 475 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 5587) covalent geometry : angle 0.77699 ( 7613) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.95197 ( 10) hydrogen bonds : bond 0.15069 ( 302) hydrogen bonds : angle 7.51785 ( 879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: R 133 ASN cc_start: 0.9205 (t0) cc_final: 0.8943 (t0) REVERT: R 162 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7903 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.1000 time to fit residues: 10.8592 Evaluate side-chains 83 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.102455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.065177 restraints weight = 11496.676| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.07 r_work: 0.2738 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5592 Z= 0.217 Angle : 0.612 7.045 7623 Z= 0.322 Chirality : 0.044 0.165 892 Planarity : 0.005 0.043 954 Dihedral : 4.276 19.401 774 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.98 % Allowed : 17.33 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.41 (0.32), residues: 708 helix: 2.14 (0.33), residues: 238 sheet: -0.16 (0.36), residues: 214 loop : -1.11 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 310 TYR 0.014 0.001 TYR C 318 PHE 0.017 0.002 PHE B 69 TRP 0.008 0.001 TRP R 139 HIS 0.004 0.001 HIS R 126 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 5587) covalent geometry : angle 0.61161 ( 7613) SS BOND : bond 0.00268 ( 5) SS BOND : angle 0.98722 ( 10) hydrogen bonds : bond 0.04272 ( 302) hydrogen bonds : angle 5.38228 ( 879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: B 151 TYR cc_start: 0.8532 (m-80) cc_final: 0.8169 (m-80) REVERT: B 200 GLN cc_start: 0.7713 (pp30) cc_final: 0.7409 (pp30) REVERT: C 347 ARG cc_start: 0.8167 (ptp90) cc_final: 0.7878 (ptp90) REVERT: C 365 GLU cc_start: 0.8496 (mp0) cc_final: 0.7968 (mp0) REVERT: C 378 ASN cc_start: 0.9220 (t0) cc_final: 0.8879 (t0) REVERT: C 422 MET cc_start: 0.9313 (pmm) cc_final: 0.9097 (pmm) REVERT: C 433 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8703 (tmtt) REVERT: R 162 ARG cc_start: 0.8416 (mmt-90) cc_final: 0.8151 (mmt-90) outliers start: 12 outliers final: 8 residues processed: 90 average time/residue: 0.1008 time to fit residues: 11.1308 Evaluate side-chains 90 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 270 MET Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.102062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.064371 restraints weight = 11364.700| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.01 r_work: 0.2725 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5592 Z= 0.223 Angle : 0.598 6.527 7623 Z= 0.312 Chirality : 0.044 0.169 892 Planarity : 0.004 0.039 954 Dihedral : 4.216 18.111 774 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.15 % Allowed : 18.48 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.49 (0.32), residues: 708 helix: 2.30 (0.33), residues: 238 sheet: -0.22 (0.35), residues: 214 loop : -1.07 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 442 TYR 0.017 0.001 TYR C 426 PHE 0.017 0.002 PHE B 69 TRP 0.008 0.001 TRP R 139 HIS 0.004 0.001 HIS R 126 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 5587) covalent geometry : angle 0.59731 ( 7613) SS BOND : bond 0.00376 ( 5) SS BOND : angle 0.86424 ( 10) hydrogen bonds : bond 0.04146 ( 302) hydrogen bonds : angle 5.05644 ( 879) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: B 200 GLN cc_start: 0.7831 (pp30) cc_final: 0.7443 (pp30) REVERT: C 347 ARG cc_start: 0.8225 (ptp90) cc_final: 0.7912 (ptp90) REVERT: C 365 GLU cc_start: 0.8522 (mp0) cc_final: 0.7902 (mp0) REVERT: C 422 MET cc_start: 0.9347 (pmm) cc_final: 0.9111 (pmm) REVERT: C 433 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8646 (tmtt) REVERT: C 435 LYS cc_start: 0.9133 (tppt) cc_final: 0.8920 (tppt) outliers start: 13 outliers final: 9 residues processed: 95 average time/residue: 0.0845 time to fit residues: 10.1731 Evaluate side-chains 89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 12 optimal weight: 0.0770 chunk 6 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 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 = 0.3624 r_free = 0.3624 target = 0.104483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.067223 restraints weight = 11352.109| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.08 r_work: 0.2780 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5592 Z= 0.116 Angle : 0.561 8.330 7623 Z= 0.291 Chirality : 0.042 0.173 892 Planarity : 0.004 0.040 954 Dihedral : 4.049 19.197 774 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.15 % Allowed : 19.31 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.64 (0.32), residues: 708 helix: 2.46 (0.33), residues: 238 sheet: -0.18 (0.35), residues: 214 loop : -0.98 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 235 TYR 0.013 0.001 TYR C 426 PHE 0.009 0.001 PHE B 69 TRP 0.018 0.001 TRP B 183 HIS 0.004 0.001 HIS R 126 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5587) covalent geometry : angle 0.56067 ( 7613) SS BOND : bond 0.00257 ( 5) SS BOND : angle 0.76480 ( 10) hydrogen bonds : bond 0.03504 ( 302) hydrogen bonds : angle 4.73963 ( 879) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: B 109 ASP cc_start: 0.9173 (m-30) cc_final: 0.8692 (m-30) REVERT: B 191 ASP cc_start: 0.8456 (t0) cc_final: 0.8214 (t0) REVERT: C 347 ARG cc_start: 0.8349 (ptp90) cc_final: 0.7921 (ptp90) REVERT: C 365 GLU cc_start: 0.8565 (mp0) cc_final: 0.7814 (mp0) REVERT: C 378 ASN cc_start: 0.9113 (t0) cc_final: 0.8767 (t0) REVERT: C 422 MET cc_start: 0.9387 (pmm) cc_final: 0.9070 (pmm) REVERT: C 433 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8569 (tmtt) REVERT: C 435 LYS cc_start: 0.9237 (tppt) cc_final: 0.8950 (tppt) REVERT: C 442 ARG cc_start: 0.7651 (mpt180) cc_final: 0.7411 (mpt180) outliers start: 13 outliers final: 8 residues processed: 85 average time/residue: 0.1000 time to fit residues: 10.5120 Evaluate side-chains 90 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.104611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.067300 restraints weight = 11470.188| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.09 r_work: 0.2779 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5592 Z= 0.118 Angle : 0.553 7.434 7623 Z= 0.287 Chirality : 0.042 0.173 892 Planarity : 0.004 0.039 954 Dihedral : 3.939 17.074 774 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.31 % Allowed : 19.64 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.74 (0.32), residues: 708 helix: 2.58 (0.33), residues: 238 sheet: -0.16 (0.36), residues: 214 loop : -0.92 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 325 TYR 0.021 0.001 TYR C 472 PHE 0.011 0.001 PHE C 495 TRP 0.019 0.001 TRP B 183 HIS 0.005 0.001 HIS R 126 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5587) covalent geometry : angle 0.55262 ( 7613) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.95140 ( 10) hydrogen bonds : bond 0.03444 ( 302) hydrogen bonds : angle 4.61661 ( 879) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.225 Fit side-chains REVERT: B 109 ASP cc_start: 0.9171 (m-30) cc_final: 0.8698 (m-30) REVERT: B 200 GLN cc_start: 0.7957 (pp30) cc_final: 0.7496 (pp30) REVERT: C 365 GLU cc_start: 0.8511 (mp0) cc_final: 0.7942 (mp0) REVERT: C 378 ASN cc_start: 0.9114 (t0) cc_final: 0.8774 (t0) REVERT: C 409 GLU cc_start: 0.9507 (pm20) cc_final: 0.9166 (pm20) REVERT: C 433 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8611 (tmtt) REVERT: C 435 LYS cc_start: 0.9217 (tppt) cc_final: 0.8935 (tppt) REVERT: C 441 ARG cc_start: 0.7967 (mmm160) cc_final: 0.7193 (tpt-90) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.0923 time to fit residues: 11.1468 Evaluate side-chains 95 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 0.0050 chunk 19 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 272 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.105654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.068242 restraints weight = 11294.173| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.00 r_work: 0.2811 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5592 Z= 0.117 Angle : 0.582 7.705 7623 Z= 0.301 Chirality : 0.042 0.173 892 Planarity : 0.004 0.039 954 Dihedral : 3.945 17.457 774 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.31 % Allowed : 20.46 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.85 (0.32), residues: 708 helix: 2.67 (0.33), residues: 238 sheet: -0.10 (0.36), residues: 214 loop : -0.84 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 410 TYR 0.022 0.001 TYR B 151 PHE 0.008 0.001 PHE B 69 TRP 0.020 0.001 TRP B 183 HIS 0.005 0.001 HIS R 126 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5587) covalent geometry : angle 0.58177 ( 7613) SS BOND : bond 0.00159 ( 5) SS BOND : angle 0.88371 ( 10) hydrogen bonds : bond 0.03347 ( 302) hydrogen bonds : angle 4.49409 ( 879) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: B 109 ASP cc_start: 0.9134 (m-30) cc_final: 0.8653 (m-30) REVERT: B 177 GLU cc_start: 0.8382 (pm20) cc_final: 0.7806 (tp30) REVERT: B 200 GLN cc_start: 0.7956 (pp30) cc_final: 0.7499 (pp30) REVERT: C 365 GLU cc_start: 0.8512 (mp0) cc_final: 0.7933 (mp0) REVERT: C 378 ASN cc_start: 0.9116 (t0) cc_final: 0.8778 (t0) REVERT: C 433 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8534 (tmtt) REVERT: C 435 LYS cc_start: 0.9256 (tppt) cc_final: 0.8989 (tppt) REVERT: C 441 ARG cc_start: 0.7586 (mmm160) cc_final: 0.7380 (tpt-90) REVERT: R 162 ARG cc_start: 0.8502 (mmt-90) cc_final: 0.8268 (mmt-90) outliers start: 14 outliers final: 12 residues processed: 99 average time/residue: 0.0898 time to fit residues: 11.0315 Evaluate side-chains 102 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 0.0060 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.2002 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.103843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.066229 restraints weight = 11452.540| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.09 r_work: 0.2770 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5592 Z= 0.161 Angle : 0.593 6.719 7623 Z= 0.308 Chirality : 0.043 0.193 892 Planarity : 0.004 0.039 954 Dihedral : 3.987 17.339 774 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.15 % Allowed : 20.79 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.82 (0.32), residues: 708 helix: 2.54 (0.33), residues: 244 sheet: -0.07 (0.36), residues: 214 loop : -0.89 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 310 TYR 0.021 0.001 TYR C 472 PHE 0.014 0.001 PHE C 495 TRP 0.015 0.001 TRP B 183 HIS 0.004 0.001 HIS R 126 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5587) covalent geometry : angle 0.59244 ( 7613) SS BOND : bond 0.00206 ( 5) SS BOND : angle 0.97875 ( 10) hydrogen bonds : bond 0.03562 ( 302) hydrogen bonds : angle 4.56006 ( 879) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: B 109 ASP cc_start: 0.9173 (m-30) cc_final: 0.8665 (m-30) REVERT: C 365 GLU cc_start: 0.8315 (mp0) cc_final: 0.7747 (mp0) REVERT: C 378 ASN cc_start: 0.9178 (t0) cc_final: 0.8824 (t0) REVERT: C 433 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8412 (tmtt) REVERT: C 435 LYS cc_start: 0.9248 (tppt) cc_final: 0.8996 (tppt) REVERT: C 441 ARG cc_start: 0.7678 (mmm160) cc_final: 0.7401 (tpt-90) REVERT: R 162 ARG cc_start: 0.8448 (mmt-90) cc_final: 0.8186 (mmt-90) outliers start: 13 outliers final: 11 residues processed: 96 average time/residue: 0.1000 time to fit residues: 12.0028 Evaluate side-chains 103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 272 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.103281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.066239 restraints weight = 11451.065| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.03 r_work: 0.2771 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5592 Z= 0.176 Angle : 0.636 10.255 7623 Z= 0.326 Chirality : 0.043 0.190 892 Planarity : 0.004 0.039 954 Dihedral : 4.020 16.951 774 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.15 % Allowed : 21.62 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.79 (0.32), residues: 708 helix: 2.44 (0.33), residues: 245 sheet: -0.06 (0.36), residues: 214 loop : -0.84 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 310 TYR 0.026 0.001 TYR B 174 PHE 0.014 0.001 PHE B 69 TRP 0.014 0.001 TRP B 183 HIS 0.004 0.001 HIS R 126 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 5587) covalent geometry : angle 0.63507 ( 7613) SS BOND : bond 0.00212 ( 5) SS BOND : angle 0.96789 ( 10) hydrogen bonds : bond 0.03668 ( 302) hydrogen bonds : angle 4.60682 ( 879) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: B 174 TYR cc_start: 0.8575 (p90) cc_final: 0.8232 (p90) REVERT: B 177 GLU cc_start: 0.8640 (pm20) cc_final: 0.8312 (pm20) REVERT: B 200 GLN cc_start: 0.7933 (pp30) cc_final: 0.7473 (pp30) REVERT: C 365 GLU cc_start: 0.8208 (mp0) cc_final: 0.7662 (mp0) REVERT: C 378 ASN cc_start: 0.9192 (t0) cc_final: 0.8846 (t0) REVERT: C 433 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8516 (tmtt) REVERT: C 442 ARG cc_start: 0.7593 (mpt180) cc_final: 0.7362 (mmt180) REVERT: R 162 ARG cc_start: 0.8462 (mmt-90) cc_final: 0.8231 (mmt-90) outliers start: 13 outliers final: 10 residues processed: 98 average time/residue: 0.0953 time to fit residues: 11.4688 Evaluate side-chains 99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.104941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.067577 restraints weight = 11246.736| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.05 r_work: 0.2791 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5592 Z= 0.134 Angle : 0.637 7.725 7623 Z= 0.331 Chirality : 0.043 0.180 892 Planarity : 0.006 0.140 954 Dihedral : 4.073 18.650 774 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.82 % Allowed : 22.28 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.87 (0.33), residues: 708 helix: 2.47 (0.33), residues: 245 sheet: 0.01 (0.36), residues: 214 loop : -0.79 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 410 TYR 0.027 0.002 TYR B 174 PHE 0.025 0.001 PHE C 495 TRP 0.013 0.001 TRP B 183 HIS 0.005 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5587) covalent geometry : angle 0.63704 ( 7613) SS BOND : bond 0.00294 ( 5) SS BOND : angle 0.89673 ( 10) hydrogen bonds : bond 0.03422 ( 302) hydrogen bonds : angle 4.49777 ( 879) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: B 109 ASP cc_start: 0.9137 (m-30) cc_final: 0.8663 (m-30) REVERT: B 174 TYR cc_start: 0.8553 (p90) cc_final: 0.8234 (p90) REVERT: B 177 GLU cc_start: 0.8564 (pm20) cc_final: 0.8267 (pm20) REVERT: B 200 GLN cc_start: 0.8019 (pp30) cc_final: 0.7547 (pp30) REVERT: C 347 ARG cc_start: 0.8291 (ptp90) cc_final: 0.8033 (ptp90) REVERT: C 365 GLU cc_start: 0.8125 (mp0) cc_final: 0.7652 (mp0) REVERT: C 378 ASN cc_start: 0.9143 (t0) cc_final: 0.8832 (t0) REVERT: C 433 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8520 (tmtt) REVERT: C 441 ARG cc_start: 0.7441 (tpt-90) cc_final: 0.7200 (tpt-90) REVERT: C 442 ARG cc_start: 0.7461 (mpt180) cc_final: 0.7195 (mmt180) REVERT: R 162 ARG cc_start: 0.8494 (mmt-90) cc_final: 0.8272 (mmt-90) outliers start: 11 outliers final: 10 residues processed: 100 average time/residue: 0.0909 time to fit residues: 11.4639 Evaluate side-chains 99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 0.0040 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.104946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.067600 restraints weight = 11326.733| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.08 r_work: 0.2800 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5592 Z= 0.132 Angle : 0.636 7.415 7623 Z= 0.327 Chirality : 0.043 0.184 892 Planarity : 0.005 0.078 954 Dihedral : 3.977 17.987 774 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.98 % Allowed : 22.44 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.87 (0.33), residues: 708 helix: 2.49 (0.33), residues: 245 sheet: -0.02 (0.36), residues: 214 loop : -0.78 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 410 TYR 0.026 0.001 TYR B 174 PHE 0.013 0.001 PHE B 69 TRP 0.032 0.002 TRP B 183 HIS 0.005 0.001 HIS R 126 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 5587) covalent geometry : angle 0.62915 ( 7613) SS BOND : bond 0.00272 ( 5) SS BOND : angle 2.68515 ( 10) hydrogen bonds : bond 0.03392 ( 302) hydrogen bonds : angle 4.45382 ( 879) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.224 Fit side-chains REVERT: B 109 ASP cc_start: 0.9144 (m-30) cc_final: 0.8656 (m-30) REVERT: B 174 TYR cc_start: 0.8496 (p90) cc_final: 0.8155 (p90) REVERT: B 200 GLN cc_start: 0.7981 (pp30) cc_final: 0.7543 (pp30) REVERT: C 347 ARG cc_start: 0.8285 (ptp90) cc_final: 0.8021 (ptp90) REVERT: C 365 GLU cc_start: 0.8062 (mp0) cc_final: 0.7577 (mp0) REVERT: C 378 ASN cc_start: 0.9168 (t0) cc_final: 0.8873 (t0) REVERT: C 441 ARG cc_start: 0.7510 (tpt-90) cc_final: 0.7292 (tpt-90) REVERT: C 442 ARG cc_start: 0.7399 (mpt180) cc_final: 0.7159 (mmt180) REVERT: R 305 GLN cc_start: 0.8462 (pm20) cc_final: 0.8238 (pm20) outliers start: 12 outliers final: 10 residues processed: 98 average time/residue: 0.0889 time to fit residues: 10.9782 Evaluate side-chains 98 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 59 optimal weight: 0.1980 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 135 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068368 restraints weight = 11404.414| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.02 r_work: 0.2813 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5592 Z= 0.131 Angle : 0.651 8.755 7623 Z= 0.334 Chirality : 0.043 0.204 892 Planarity : 0.006 0.126 954 Dihedral : 4.021 19.879 774 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.82 % Allowed : 22.77 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.89 (0.33), residues: 708 helix: 2.49 (0.33), residues: 245 sheet: 0.02 (0.36), residues: 214 loop : -0.78 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 410 TYR 0.028 0.002 TYR B 174 PHE 0.013 0.001 PHE C 495 TRP 0.027 0.001 TRP B 183 HIS 0.005 0.001 HIS R 126 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 5587) covalent geometry : angle 0.64717 ( 7613) SS BOND : bond 0.00181 ( 5) SS BOND : angle 1.98918 ( 10) hydrogen bonds : bond 0.03337 ( 302) hydrogen bonds : angle 4.43712 ( 879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1455.47 seconds wall clock time: 25 minutes 42.49 seconds (1542.49 seconds total)